I’m sorry! I didn’t proofread my post enough 
I meant that it will work now if I create a new brush present or overwrite an existing brush present while the brush tips are already within a subfolder in /brushes/. I’ve also tested that palletes, gradients, and gamut masks successfully read from subfolders too
I think that I discovered another bug where if a resource is moved out of a subfolder or moved into a subfolder, Krita won’t read the resource from it’s new location unless the “resourcecache.sqlite” is deleted. When the resource is moved back into it’s original location, Krita can read it again without having to delete the sqlite file.
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For example if the palette file “concept-cookie.gpl” was moved from /krita/palettes/ to /krita/palettes/subfolder Krita won’t read it anymore until the sqlite file is deleted and regenerated.
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But if it was moved back from /krita/palettes/subfolder to it’s original location /krita/palettes/ Krita will read it again without having to delete the database file.