Faced more or less same problem myself: modified my new trailer so it could hold H16 when disassembled. Must admit a large part of my cargo capacity (10' box on trailer) got lost to store all the metal sections of the trampoline, rudders, sail etc. (Due to shape impossible to store economically, heavy stuff too) Fixed both hulls rather high (± 5 feet) which meant weight lifting !! Od banana shape with studs sticking out nasty. Definitely not an easy shape to fix firmly. Try this before with a single hull on a flat area, you will be disappointed!
Resuming: I disassembled my Hobie to avoid driving 2x 1700 km across Europe with a 8 feet wide trailer but found the advantage doubtfull. Lot of additional work and probably most important: the weight of both hulls high on the trailer made it feel unstable (and caught a lot of side-)wind. Needed also at least 3 people to lift hulls on the frame. Don't know how high you will have to lift the hulls to put them on your roof but I would recommend a try-out first. If it's going to be a regular job, I would reconsider seriously. Or buy a Dart or Top Cat instead (more easy, less part, less weight).

Hobie 16 #99173
The Netherlands
Europe