Should modifiable items in a savable inventory be RefCounted or Resources?

Make it a Resource. The only draw back for you would be that Resources take slightly more memory than RefCounted, but unless you have actual performance issues, you shouldn’t worry about that.

Then you have all the benefits that come with Resources, the main one being able to view and edit it directly in the Editor.

Difference between a Resource and RefCounted is not that big as between a Resource and a Node.
Check this post out, it’s really insightful.