After having thousand of libraries loaded by plugins may not be a good thing
That’s simply reuse, and is no different from what is done e.g. by npm in the web world. Or or opening a command shell and having thousands of command line tools at your finger tips.
I’m working for a company who have python integrated into a large machine controlling system, and our use of python goes much deeper than it’s use in Krita. The number of packages used by our python script is really the least of our worries. 
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I see lots of potential use for python for Krita for end users, from everything from AI and super resolution, to doing GMIC like modifications of the image. I therefore think it is a shame that third party python library use is discouraged instead of changing the infrastructure to accomodate it.