You raise a good point. It's hard to say for certain how bullet arts affect move staling seeing as they are a unique character trait to Bayonetta but I believe it will work somewhat similarly to how multi-hitting attacks affect staleness. That being a move like Greninja's up aerial when: either all hits connect or only he cancels the move prematurely by fast-falling to the ground, both cases count as a single entry to the stale move list. This suggests to me that when Bayonetta holds down jab 1 and shoots multiple bullets at the enemy it still only counts as a single entry of jab to the stale move list regardless of how long you hold the button for. If this is the case then in order to unstale your killing moves the quickest you would have to input separate jab (or other non killing moves that have bullet arts) commands which has the potential downside of leaving you more susceptible to attacks because of the startup/endlag of the moves you repeatedly input.
There is, however, a character in the roster does have a way to unstale moves very effectively and has been able to do so in every smash title hes been in. Each button press of Fox's neutral special that connects with an enemy hurt-box counts as an individual entry into the stale move queue. In my testing Fox's fully staled up smash kills Megaman at 134% in the middle of final destination. But after 9 inputs of neutral special up smash kills at 106%, 28% earlier!
If Bayoneta's neutral special behaves like Fox's in that she continues firing as you mash the button then this can be a very practical way of refreshing her stale move queue. I will definitely be labbing with her on release, until then we wont know for sure.
This video provide clear insight into how the stale move negation mechanic works. Its is definitely worth a watch if you haven't seen it.
https://www.youtube.com/watch?v=Wis_25jQeew