I installed Quark to use some of the feature tweaks, but I don't want to use the wood/stone variants, decorative blocks, etc etc. I disabled them in Quark, but the blocks I can't use or craft are still showing up in EMI.

Is there a way to hide them without manually clicking them all in EMI? Shouldn't they be hidden if they're disabled?

that is normal. Jei only shows stuff in creative tabs. EMI wont, not by default at least. I think theres a config for it