Deleting system fonts seems impossible, Windows is preventing it.
In order to update to Paint.net v5.0.11, I need not just any Windows 10, but Windows 10 update 1809. I'm currently on Windows 10 LTSB update 1607, and updating any Windows from LTSB branch is basically a complete re-installing Windows system. Seems a bit too much just for newer version of Paint.net
But still - thanks so much for clarification, at least now I know that I need to just stop trying to find a way to hide fonts from "outdated" version of Paint.Net