I agree with most of this except I'd prefer actually addon_registry hooks get smaller, not bigger. Just make a new hook type.

How about we put them in the info functions of the modules instead, since that's where the tables get created anyhow?

It uses considerable memory loading up metadata from a lot of files. We have a hack to pull in individual functions from classes so we don't generally take the hit of parsing all the PHP files at once, but even then we don't want to have information in there that is only needed for obscure stuff like docs generation or testing.