It looks like you're new here. If you want to get involved, click one of these buttons!
You do not want the core material to get waterlogged, lest everything under the gelcoat turns into a nasty fungal goo. Nomex core layups will soak up the water like s sponge. If you are not going to fix it right away, and it is a low wear area, try sealing it temporarily with silicone sealer.
I am not terribly familiar with the fine points of J-bars - we spend a brief time playing with saddles and rollers and then went back to old-fashioned stackers (for all and any kinds of kayaks). But one thing I noticed in the photo was that I couldn't see a thick wad of anything between the boat and the Jbars. It may just be that this boat carries better if some good pipe insulation is added to the bars at the bottom, to absorb the shock of the rear end bouncing around.
Another option if it is physically possible may be to move the boat a few inches forward, to reduce the bounce over bumps on the back end, but I can't tell if you actually have room to do that from the perspective on the photo.
This may be a hairline crack that no one could have ever noticed, and trailering gave it just the right hit to make itself known.
A potentially huge problem is that your trailer is not providing any shock absorption as does the suspension of a car. With that combination of wheel, spring, and axle, you need 500+ lbs on it just to smooth out the ride. I tried this (including taking the extra spring leaves out) and it still beat the hell out of the boats.
Speaking from experience, I would not haul a composite boat on a trailer like this, unless it was one that I didn't care for very much.