A related question might be "do you close your EXHAUST outlet"?
Mine is on the starboard side close to the waterline...not in the stern as with 95% of the boats out there...and I can see a hard heel to starboard perhaps forcing water up the modest incline and back down to the waterlift.
I have heard that following seas are occasionally a problem with stern-exhaust boats in that water can be forced up beyond the usual loop and back into the 'can", making for nastiness of a distressingly familiar type.
As for the raw water intake, on the new boat I have a fresh water circuit and a Perko strainer glass on the raw water circuit mounted fairly high. The water has to climb and fall a bit before it even gets to the raw water pump, so I don't worry much.
On the old boat, I left it open underway, but closed it and all other seacocks when away from the boat, except for the cockpit scuppers. I've seen more than one boat sinking or sunk at dock due to a failed hoseclamp or hose in this particular area. I simply hang the starter key on the thru-hull handle.