I’ve excluded them on all my machines. Interestingly, M1 machines no longer seem to have any issues, but my Intel work machine still occasionally double pastes!
Java apps do tend to have this sort of problem occasionally, I’ve been tackling a memory leak issue in it, so I’d be surprised if the culprit really was PopClip, but I also don’t need PopClip in my IDEs so it makes sense to exclude it!