It depends what your hull is made of.
If it's metal, or Carbon Fibre, or anything that shields RF radiation, your aerials need to be uncovered. If it's wood, plastic, GRP, glass-fibre or anything that lets RF through, they can be completely enclosed in the hull.
It's generally a good idea to have the aerials as high up as possible. There is some concern that if you have a receiver well under the water-line then it might not get enough signal if it's 2.4Ghz, since that frequency does not pass through water very well. But other people have said that they have not found low aerials to be a problem…