Two formats are always more difficult than one.
If you can get every other mod/script/addon writer to use JSON for thier flat files, then no, it's not any more difficult.
Remember, we still have people confused going from release to SVN ULib storage. I can't imagine the additional support hour nightmare going to yet another, actually bigger, change.
If the other mod writers use it for flat files, it becomes 'same or easier'.
If not, that means more work for us on the support role. Sure, validators are great, but we still get questions of "the validator says it's not right...why not?"
Right now, many already are using sqlite.db, SQL, or text lua key value files.
Throwing one more configuration type into the mix (JSON) just doesn't seem logical, tools to assist or not.
I think you may just as well spend your time writing a Lua key value flat file validator.
I'm not saying JSON is bad. It would be great for other projects. I just can't imagine it being good in the Gmod world of ULib.