Guardians are not spawning in Water Monuments, but the Elder Guardians are.

EDIT: Upon further review, the issue here is that the Vanilla spawn rules for DEEP OCEAN have been over-written by TC, not allowing the Guardians to spawn in the water areas surrounding any included water monument. By removing TC after world generation, the vanilla spawn rules produce Guardians at a normal rate. Re-enabling TC, prevents spawns again, and spawns skeletons, creepers, spiders, endermen, zombies, etc. in exposed, non-water filled areas.