I guess that doesn't matter too much.
The bottom line is that water has probably been sitting there for a while. It partially depends on what wood the floor is made out of. Ply wood tends to deteriorate a lot slower than that partical type shit some people use (i dont know what its called. looks like its made out of a bunch of pieces and chips of wood bonded together). It sounds like the wood hasn't rotted yet, so i would say your could let it dry out a bit and then put whatever over it ensuring it is sealed propperly.
Although the best bet would be to replace the wood. Its not too hard, pull the nails up, then the board. Cut a new one, and nail it back down.
Anyway, i'd say you're probably alright. Especially if you're laying tile over it, since you'll be using concrete board anyway. This is assuming the wood is not already rotted.
I haven't laid the vinyl tiles, but you might try using some self leveling concrete if its not even. Its pretty easy to use and doesn't take too long to set.