That works as well, but at that point you might as well just use epoxy resin as the paint is not cheap either.
Also kayaks are not kept in the water full time like most runabouts.
It's long term exposure to water that is the problem.

yeah you could use epoxy resin but you still need to apply a final coat of the epoxy resin or paint to finished fiberglassed surface to seal it. If you use polyester resin you'll need to apply some kind of epoxy pant to seal it. Basically the same deal, however I believe the epoxy resin will stick better to wood and last longer.

I do know that fiberglass can rot if not properly protected so I'm assuming something is needed.

I've built a cedar strip canoe covered with fiberglass cloth, two part epoxy and marine grade varnish on top of that. Once the two part epoxy is fully cured it is inert, waterproof and can't hurt anything unless you sand it. Like any fine sanding dust, you need to protect your lungs from that. The varnish is there for UV protection otherwise the epoxy will eventually discolour and deteriorate. You wouldn't need the varnish for your application and I'm not sure varnish would be safe in a reef tank either.

The two part epoxy I used is "West System" and is fairly costly but you wouldn't be using nearly as much as I did for the boat. I think there are cheaper alternatives, but I haven't looked into those.

http://www.westsystem.com/
http://bearmountainboats.com/building_materials.htm

Not sure what kind of resin you're planning to use, but I'm fairly certain the two part epoxy is safe.