Tried several installations to see if maybe it was some weird conflict, but disabling mod content seems to have no effect at all. Items are still craftable and they still show up in JEI.

Same here, so it can be replicated.

I have a version in dev which does this differently. Not sure what items were still craftable, but they shouldn't be and they will no longer appear in JEI and nor will recipes related to blocks / items that are disabled.

this is now fixed in the latest release on curseforge