Should be about something else than ToS, the quote is talking about a contract. The news is not sufficient to understand what supposedly happened there. That the Youtuber had a contract with Youtube, is that common? Maybe the court judged the partner program agreements as one?

That "future changes may apply without notice" is invalid in Germany, that's evident. Companies writing bullshit like that in AGBs (ToS) or contracts don't realize Germany is not the US, they need a new legal team.

If the news is correct you are right about the fine being about ignoring the court, not about removing the video in the first place. With a fine that high it has to be about that, there is no way removing a regular video could cause this. Basically the court saw youtube in contempt of the court, kinda.

Might also be politically charged though, East Germany is highly penetrated by Nazis and with a high percentage of corona deniers. Depends on the judge of course whether that was a factor here.