It actually didn't happen a lot, historically? Brothers and nephews, all the time (although even then it was often controversial; the "disappearance" of Richard III's nephews was one of the main reasons he was overthrown), but their own kids, very rarely.
Contrary to what CK2 tells you, the majority of medieval rulers didn't actually spend most of their free time plotting to kill close family members with exploding manure.
We have no idea how often children where killed by the rulers.
They had the means and the power to cover up such actions, and probably only unlucky ones got exposed and history got a chance to tell us about things going on.
But most cases happened without anyone taking notice.
Besides, in those times kid mortality was incredibly high and nobody would suspect if you lose some children because of diseases or some accident.
The game follows that path. All plots are including covering up stories so it "would look like natural death" etc. And only if one of your co-plotters talks in public or alcohol makes the tongue loose the plan gets revealed.
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Historically, I have to remind of Ivan the Terrible, Moscovite Great-Duchy. That is not exactly CR2 time frame, but in a culture that was far behind compared with Europe, it still can be regarded as medieval. And it is also a case which shows that if you are feared enough by your people, a killing or two of your kinsfolk does not mean added risks for you. As Ivan Grosny did far more things than killing his son, like beheading thousands, mass-raping women (even of nobility) and what else... They even did not mind his madness.