Yes, the scupper should work just sitting in the water...
Scupper valves are simple things that work via differential water pressure. If you have water in the passenger compartment, it is (hopefully! {grin}) higher than the outside water and therefore exerts pressure on the valve so it can seek its common level and flow out. Once the levels are equal, there is no outbound pressure so the valve should close on its own.
Rain or snow accumulating in the passenger compartment can slowly fill the scupper hose, eventually exerting enough pressure to open the valve. Lather, rinse, repeat.
On the other hand, if you have a leak that leads into the bilge (engine compartment), that's BELOW the waterline and therefore requires some sort of assistance to get out. Hence your bilge pump, which is generally wired around the main battery switch so the boat will stay afloat even if "everything" is turned off. At least until your battery dies, at which time if you're still taking on water your boat will slowly sink. Long before that, though, you'll submerge your engine(s) and have a whole new boat restoration hobby.
Bottom line: If you leave ANY boat docked in the water for extended periods, you need to make certain your battery stays charged, and that you minimize any entry path for water into the bilge.
