Other than fleet weaponry, I haven't seen a single anti-proton space weapon drop ever yet the tactical consoles still drop for them. Why get rid of the weapons drop at all?

You need to craft them. I crafted six MKXI Anti-Proton Beam Arrays Crit DMGx2 for my Odyssey. It's amazing to melt Borg Cubes by yourself in Elite STFs.

they need to drop....

I would love to see Antiproton Beam Array Mk XI [Acc]x3 drop along with the other preferences in Drop Suffix's.

Crafting them is still an idea, but for what used to be and by all definition a standard ship weapon they should be dropping like so many other standardized weapons and not treated as though they are something unique.

It seems MK XII is actually supposed to cost Dilithium now - so the fleet store is your best bet.