The space borne planetary invasion force is a staple of many Sci-fi genres and most space invasions face the need to destroy some, or all, ground based infrastructure from orbit in order to take over a world. One of the things that often puzzles me is the depiction of lasers or particle beams for targeted ground attacks. These weapons would seem to tend to be dispersed or deflected by atmospheric gases and planetary magnetic fields.

Assuming:

• that orbital dropped munitions are at least as accurate as modern smart bombs.




• that you have access to "dialable damage" kinetic weapons for attacking ground side infrastructure.




• that you want the planet you've gone to the trouble of invading largely intact, so no cobalt bombs or other long-term area-denial weapons.




• that these weapons, while extremely useful for hammering planetary targets, are too slow moving for ship-to-ship combat and as such are not used as combat vessels' primary weapons.




• that such weapons are not excessively large and can be mounted on/carried by warships without compromising their primary mission capability.




• that planetary bombardment is rare in other circumstances but almost always necessary to support invasion forces.

For what practical reasons would weapon systems which are more suited to ship-to-ship combat be used in this planetary mass destruction role when they appear to suffer issues of accuracy and loss of power due to atmospheric effects and possibly cause excessive/secondary damage effects as a result of either heat bloom or, as in the case of nuclear or particle beam weapons, the nature of their operation?

Because they are the most efficient way to deal damage to your specific target

An (arguably) non-kinetic bombardment weapon would be an antimatter beam, which is a great opportunity to commit genocide..., no!!! cleanse heresy, no!!! strategically secure the target yes!!!. You did say that the planet should be captured intact, but there are many levels of intact. Especially if you are dealing with a hostile biosphere or some biological enemy like the Tyranids or the Zerg, keeping the atmospere at a toasty 500 C for a few days before landing should help. Antimatter beams would probably be best for this, but lasers whose energy will be absorbed by the atmosphere will do great as well.

Because Ammunition is more (mass) expensive than reactor fuel and radiator time

Remember the rocket equation? Everyone in space does. Maybe it is just more efficient to carry around the reactor fuel to power the energy weapons than it is to carry missiles and uranium enriched tungsten speers. While in a space battle radiator time is a valuable resource, during a bombardment taking care of heat is simple.

Kinetic weapons are energy weapons

Maybe your military avoids many issues (waste heat management) shipboard energy weapons bring with them and uses missiles with nuke-pumped-x-ray-laser or casba howitzer warheads (nuke-pumped particle beams). For planetside bombardment they are used as an energy and kinetic weapon. They fire the energy-weapon component to blind the target and hit it then with the high speed shrapnel the missiles husk has turned into.

Because energy weapons are what the vessels carry

This is based on the rocket equation again. Every gram counts on a spacecraft. The military may have access to decent kinetic weapons, but if they are as you say useless in vessel to vessel combat (I do not think the are, but it's your universe) carrying them around is simply too costly delta-vee wise.

The real reason why popular media shows this

Hollywood has no clue about Hardish Sci-Fi. Lasers look cool and cool weapons are better war-maschines than realistic ones. Visually colourful laser beams are more impressive and easier to produce than depicting missiles and kinetic slugs. Star Wars and Star Trek did it and have influenced most subsequent Sci-Fi. Audiences and lazy writers know it and love it and thus a vicious cycle ensues.

Economies of scale matter on warships too

If you look at naval vessels throughout history, they have always tended to evolve towards specialization in weaponry. The more different kinds of weapons you have, the more complicated your maintenance, logistics, and even design and construction of your ship get. This is why it's very rare to see a warship of almost any era with multiple primary weapons systems. The best designs pick one thing and do it as thoroughly as possible.

In response to your question, the simplest explanation is that the PRIMARY role of the space battleships is destroying other space-based defenses and that is best accomplished with directed energy weapons. Once that has been accomplished, the actual orbital bombardment is a secondary task, and the weapons you're using only have to be 'good enough'. Adding specialized planetary bombardment weaponry would make the ships LESS capable at defeating the space-based defenses, so you're better off specializing your ships for space combat and accepting that your bombardment is going to be a bit less effective.

EDIT:

Assume... that such weapons are not excessively large and can be
mounted on/carried by warships without compromising their primary
mission capability.

I'm going to challenge this item in your post because you can't have a realistic discussion about military engineering with an assumption like this. Nothing is free in engineering, and there's no such thing as a weapons system that doesn't contribute to the primary mission of the platform that DOESN'T compromise the primary mission capability to some degree. It's always a question of 'how much' does it compromise that mission capability.

Remember we're not JUST talking about mass, or power consumption, or any of those things. Adding extra weapons makes the ship more expensive. It makes it more complicated. It means you're mounting this kinetic weapons system INSTEAD of something else that WOULD contribute to the primary mission and that is never beneficial.

Here, again, if the primary energy weapons systems on the warships are capable of performing the secondary planetary bombardment mission adequately, it doesn't really matter if it's a small compromise versus a large one to mount a separate kinetic bombardment system, it's still unwelcome and makes the ship less effective than it could be.

Particle beams are a nice clean way to eradicate life forms.

Neutrons are uncharged particles and so will not be blocked by a planetary electromagnetic field or shields relying on that sort of thing. This is true for heavier particles too. In this question What subatomic particle is best for a particle accelerator gun? I figured that radon particles would be the best for delivering energy that would penetrate intervening matter (here atmosphere) and drop off the energy within a calculable area (where your enemies and their pets live).

The neutron bomb claimed some fame because this type of radiation would supposedly kill everything but leave buildings, weapons, sports cars intact. Rods from god do not leave infrastructure intact. If you want to reclaim your holy sites, or take over the phlogiston mines, or drive around in sweet enemy sports cars you can't turn them into craters. Uncharged particle radiation would be a fine way to eradicate life from the area. A beam instead of a bomb also reduces residual contamination from radionuclides generated in the explosion.

Note: you might need to give the particles time to work. They probably will not kill everyone outright but should within the next couple of weeks.

Kinetic weapons can be intercepted.

If you have lasers capable enough to engage in ship-to-ship warfare and punch through atmospheres to destroy ground installations then surely those ground installations have lasers capable of destroying falling rocks. What would be the point of constructing planetary defenses if they weren’t capable, at the very least, of defending against the most effective and economical method of attack? Lasers and particle beams, on the other hand, cannot be actively intercepted.