No fire suppression, the floor boards are supposed to be sealed, do not know how watertight the hatch is. The avionics racks usually have a cover. Bravo on your action (pulling the shroud).
I once launched a 742F that was loaded in heavy rain, one generator inoperative. About an hour into flight they lost 2 more generators (water contamination of the generator control units in the E&E) limping back home on only one. 99.9% of the time water entering the E&E will have no effect, it is quite common on freighters. None the less it should be addressed with serious caution every time.