Assuming a 2.4GHz radio, as long as whatever structure is between the antenna and the outside world does not blank the signal, under the deck is fine. Wood, plastic are generally transparent to radio signals, metal isn't.
Siting any component where it is inaccessible for later work is never a good idea, especially a radio. If it ever needed rebinding (say, if a new transmitter was got) and you couldn't reach the bind button or access the bind pins easily, that would be a disaster.
Older type radios work OK with the antenna around the deck edge, but do get better range if vertical. On a small model the extra range is usually surplus to requirements, on a larger model a vertical one can be "lost" easily enough, but does not need to be fixed to the receiver - it can have a plug in line.
Only the end 1" of the 2.4GHz antenna is used as a signal pick-up, and must be straight. The black part is a co-ax cable connecting receiver and actual aerial. The long aerial wires of older systems work best if straight and vertical, still work OK horizontal, acceptable if scrunched in an untidy manner above the water line, and "sort of" work if tidily coiled, when they effectively become an in-line choke.