We use MIG because we have it and using 3/16 ths we wanted the strongest welds we could get. Also, some of the designs we're trying only allow welding on one side in some areas so we wanted good penetration and wide, well bonded welds. For construction of most loaders Stick or TIG is fine, obviously the penetration must be set correctly and proper weld material used.
As far as rusting ... we clean and spray coat our loaders with graphite before every race and every time we change them ... but that's for racing. For the lake or river, I would simply drop the loader at the start of every weekend before leaving the house, clean and inspect it then spray paint it to protect it and go and have fun ... I would change the #8 black loader bolts as needed or a couple of times a season as they are under considerable stress when the boat is running. When inspecting the loader should you spot a cracked weld or broken piece you should change it before taking the boat to water.