I think just carrying the dependencies in alongside the plugin to be the best, most people will be lost trying to do a pip install of the dependencies on a custom folder for krita.
I have to checkout your plugin but by what you said you might need to explain how to do a install properly.
I know people that are great artists but downloading from GitHub is already a complicated thing to do already.
For mine I just ported or adapted the code or recreated stuff from scratch, but your case will have versioning which will be worse. Math does not have versioning.
Also the more dependencies you place the slower things will become inside Krita. Integrating them in your code speeds things alot.
Ps. Also found this