Submerged or inline make no difference in noise, but you need to be more careful when you clean the pump if you use it inline. The pump head housing is very fragile, and if you crack it, it will leak. It is also prone to salt creep if you don't tight it enough. The rubber gasket is not the best one around, you know. But if you tight it too much, you will crack it. Catch-22, sort of.
IMHO, the best pump head are made of good plastic. Nylon is too soft for my taste (little giants), but it is alright. Go with the same material as Iwaski pump and the likes if you want good engineering.