You are right, every time you create a new layer in Animation Paper it just names it with the next number – regardless if any layers have been deleted and therefore “freed up a number”.
This is, I think, the preferred behaviour. My thought was that you could potentially get confused with a new layer named the same as one you had earlier. Of course you risk having “holes” in your layer number sequence, but if we start filling a “hole” you will end up adding layers with numbering out of sequence. So there are pros and cons.
I do believe it is not that important either way (as you suggest yourself) – because I think you should call your layers something more descriptive anyway. But of course that doesn’t mean the automatic naming shouldn’t be optimal. Let me know if you feel strongly about your point and feel free to give me more reasons why we should change it.
Thanks a lot!