I discussed this with the Krita devs and this will not break anything. The developers themselves use multiple versions of the AppImage and Flatpak at the same time and they all use ~/.local/share/krita/ for resources without any issues. Krita just ignores any resource it does not understand.
The Krita developers already support running multiple versions of Krita at the same time, so the snap will not introduce any new or unknown behavior.
One issue came up about a possible future version of Krita, although this is still subject to change. They are currently rewriting the resource manager and the current design includes some changes which require a one-way migration. In the current plans, the new version of Krita will do this migration when it starts. After this migration, older Krita versions will still work but some specific types of resources will not be accessible anymore because their subdirectory changed during the migration. Edit: the Krita developers made it clear that they want to fix these issues before it’s released, and running multiple versions of this resource manager will be possible.
I also want to point out that special care was taken in the resource manager to make sure users don’t accidentally lose resources, even if Krita itself contains a bug. For example, when resources are deleted, they are not actually removed from the filesystem, they are simply marked as “deleted” by Krita, but users can still recover them manually from the filesystem.
See the conversation on the Krita forum for more info.