The drum kit itself doesn't care. It's the data that's being inputted into the synth that matters. If that data is 4/4, then I think that 4th beat would technically land on the 1st beat of the 3/4 measure, and would keep looping like that.
If you've found a 4/4 beat that you like, but want to amend it to a 3/4, you'll probably have to go into the MIDI Piano View and delete the 4th quarter of the loop. If I'm understanding the issue properly.