Mdthbs

As seen from this question, the Heavenly Court does not punish an individual (at least in this life) if he or she is under 20.

However, according to Seder Hadoros (Year 2217) Er and Onan were 7 or 8 years old when G-d slew them for wasting seed.

So, if the Heavenly Court does not punish individuals under 20 why were Er and Onan punished when they were only 7 or 8 years old?

This exact question was asked by the Tosafist R. Yehuda Ben Elazar in his commentary to Genesis 38:10:

וא"ת למה נענשו ער ואונן והלא לא היו אלא בני ח' שנה כדאי' בסדר עולם ואמרי' בית דין של מעלה אין מענישין עד כ' שנה ותירץ ר' יהודה החסיד דאין הדבר תלוי אלא בדעת ובמחשבה כי יש פחות מי"ג שנה ערום בדעת ובמחשבה לרעה או לטובה

Why were Er and Onan punished? Weren't they only 8 years old as [mentioned] in Seder Olam, and we say that the Divine Court doesn't punish until [the age of] 20 years?

And R. Yehuda HaChasid answered that the matter is only dependent on intellect and thought, for there are those younger than 13 years who are subtle in intellect and thought [whether] to bad or to good.

Another Tosafist, R. Avigdor Tzarfati, asked the same question and gave the same answer and also suggested an additional answer:

וקשה והלא ער ואונן לא היו כ"א בני ח' שנים או ט' ולא הגיע עדיין לכלל עונשין א"כ למה נענשו והא אמרינן דאין עונשין מלמעלה אלא מבן עשרים וי"ל כך דיני שמים דעונשין אדם לפי חכמתו בין שהוא גדול ואם קטן בן ט' חכם כבן עשרים עונשין אותו וראיה משמואל הנביא שרצה עלי הכהן להענישו בעבור שהורה הלכה בפני רבו אע"פ שלא היה כ"א בן ג' שנים [עוד י"ל] דהא דאמרי' שאין עונשין מלמעלה אלא עד שיהא בן כ' זה ר"ל בגזירה גזירה גדולה כששופט אומה אחת ביחד אז מונה מכ' שנים ולמעלה ודן אותם אחר הרוב או לעתיד לבא (כשיצא) [כשיצחק ימליץ] טוב על ישראל אז לא יזכור אלא מבן כ' ולמעלה אבל אדם אחד אפי' פחות מי"ג עונשין אותו למעלה וכן לטובה

And it is difficult – weren't Er and Onan only 8 or 9 years old, and they hadn't yet attained punishable status? If so, why were they punished? We say that Heaven only punishes from age 20!

We could say that the rules of Heaven are that they punish a person based on his knowledge, whether [or not] he is an adult, and if a 9 year old minor is as knowledgeable as a 20 year old they punish him.

And the proof is from Samuel the prophet, for Eli the priest wanted to punish him for ruling on a matter of law in the presence of his teacher, even though he was only 3 years old.

We can further say that that which Heaven doesn't punish until age 20 is when there is a major decree and a nation is being judged as one. Then they count from 20 years and above and judge them based on the majority. Or in the future when Isaac advocates in defense of Israel then they will only mention from age 20 and above. But an individual person even younger than 13 can be punished by Heaven, and the same [applies] for good.

In Kallah Rabasi 4:6
it mentions the fact that Er and Onan were punished by heavenly court, followed by the fact that children can reach lofty levels. The Nachlas Yaakov, a commentary printed on the side there in the Gemara, writes that the connection between the two points of the Brasisa, is to answer your question. The reason why these children were punished, is because if they were advanced enough to reach high levels, they are mature enough to be punished as well.

ונ"ל הא דמייתי האי דרשה הכא בא ליישב שלא תקשה היכא ילפינן מער שחייב מיתה הא ער ואונן קטנים היו וא"כ ע"כ לאו משום חטאן מתו דלאו בני עונשין נינהו מש"ה מביא ראיה דקטנים מקבלין פני השכינה וא"כ מסתברא דנענשו נמי כשיחטאו

This question was asked by many authorities. For example, the Chacham Tzvi § 49.

He says that there are those that suggest it was because of their intellectual maturity. Even though they were minors, they were mentally responsible for their actions like an adult. The Dovev Mesharim ed. of the Chacham Tzvi points to the Sefer Chassidim (Makitzei Nirdamim ed., based on Italian manuscripts) § 217 who says this answer (you can also see a different version quoted in @Alex's answer).

קטן שחילל שבת אינו נהרג וקטן שהורה לפני רבו חייב מיתה כשמואל לעלי, אלא כשאמרה חנה (ש"א א כז) אל הנער הזה התפללתי, הרי משמים מענישין קטן הואיל ודעתו כגדול כער ואונן

However, the Chacham Tzvi rejects this approach. Instead, he wants to limit the scope of this concept. He gives four approaches on how to limit it (see here for a summary), as he is bothered how could someone commit crimes as a minor and not be punished in the world to come. However, three of them don't address Er and Onan. The one that does is that the concept that Heavenly punishment is only above twenty is that we sometimes see this to be true.

Someone I found who tries to use the Chacham Tzvi's rejected approach is Rav Dovid Kronglass (former Mashgiach at Yeshivas Ner Yisroel) in Sichos Chochmah UMussar II § 50. He builds off the Chavos Yair § 166, who explains this concept to only apply to "mitzvos sichliyos", intuitive mitzvos. Something someone can figure out on their own, they're punished for, even as a child. He gives the example of machlokes, where we see the babies of Korach and his assembly were punished. This is pointed out in various sources:

Bamidbar Rabbah 18:4; Midrash Tanchuma Korach § 3:

כַּמָּה קָשָׁה הַמַּחֲלֹקֶת, שֶׁבֵּית דִּין שֶׁל מַעְלָה אֵין קוֹנְסִין אֶלָּא מִבֶּן עֶשְׂרִים שָׁנָה וָמַעְלָה, וּבֵית דִּין שֶׁל מַטָּה מִבֶּן שְׁלֹשׁ עֶשְׂרֵה. וּבְמַחֲלֻקְתּוֹ שֶׁל קֹרַח, תִּינוֹקוֹת בֶּן יוֹמָן נִשְׂרְפוּ וְנִבְלְעוּ בִּשְׁאוֹל תַּחְתִּית

How harmful is dissension! An emissary of the court on high only imposes a penalty [on people] from the age of twenty years, while the court below [only imposes a penalty] from the age of thirteen years. In the case of Korah's dissension, however, one-day-old babies were burned and swallowed up in nethermost Sheol

Machlokes is intuitively negative. However, prohibitions that are explicit are equally punished by Heaven and Earth starting at the ages of 12/13. Rav Kronglass says the Chasam Sofer (YD 155) writes somewhat similar to this:

בשרה נאמר בת עשרים כבת ז' בלא חטא התם קודם מ"ת הוה והכל אצלה כמצות שכליות וע"ז נאמרו שיעורי' הללו

As well, Rav Kronglass points out that this explains why children died during the flood, and why children in Sedom were punished. Both those events involved mitzvos sichliyos.

Rav Kronglass takes this differentiation and uses it to explain Er and Onan. He says that it can't be that their sin was part of the mitzvos sichliyos, so that means someone thirteen and above should be punished by Heaven. However, as you pointed out, they were even younger than that. He says that their intelligence was that of someone over the age of thirteen, so they were punished by Heaven by that standard.