I don't think Citra was the target. I think this was all because of the "Switch 2", which is probably very similar to the Switch we have now. If they want the next console to be backwards compatible with the Switch, which has a bazillion titles for it, then they're also opening the door for something like a ntrboot hack. You'll notice that they delayed the announcement of the next console to next Spring at the same time they started going after Yuzu and some of the hacking software for the Switch.
Now, having said that, considering the Citra Team were issuing updates right up until they announced their agreement with Nintendo, and it was an agreement done completely outside the courts, makes me think there's more to this than what the press release said on the subject. Citra was never a part of this right up until the agreement. Consider this, there's SNES emulators for the original DS, yet the SNES Virtual Console titles can only run on a New 3DS. If they want their next gen console to have 3DS titles on their Nintendo Online service, Nintendo now has the code to do that.
Since there's absolutely no reason to take Citra down, but the Citra Team took it down along with Nintendo, and this was done very quickly(Citra and Yuzu were updated over the weekend before the agreement) and outside of any public court record, I'd be willing to bet that Nintendo either hired the core Citra Team or bought their work despite what both sides said publicly.
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