I like them on the outside of the hulls, yes salt can be a concern. Look at all the carolina boats that have them on the outside of the hull. I've had them on two boats now and really can't say much about the salt intrusion. Just make sure you put a couple 90's in there. You can really quiet the boat down if you plug up all the little noise intrusions from the cabin, etc. So many times on boats you can hear the engine drawing air from the cabin with that high pitch whistle etc. When a boat is tweaked in, it makes those multiday trips much easier.
I've been debating putting in an air vent on the stern of the vessel, with a drainage box back overboard. I really like to vent under the cockpit and do not like like the noise. Best thign I've noticed is open up a hatch in your cockpit and that engine noise you'll get in the boat. Granted you can cut down on the noise with 90's, or so I believe as I've always seen them there but also have to imagine it cuts down on the air flow to some level but to what level never been able to get anyone to dial it in.
Sadly, two downeast boats I've had, have had problems with the cockpit deck and people keep pointing to not enough ventillation back there, yes the wood was glassed boat sides, etc.