Are your temperatures very high? Are you also getting rain?
I think nitrates that are too high or fluctuating can cause the same thing in aquaponics or hydroponics. You might just need to feed less.
I've had tomatoes splitting due to high temps with direct sunlight and sudden rain. I may be wrong about the diagnosis, but i have observed this a few times.
Tomato splitting has to do with water fluctuations. If there hasn't been a lot of water available and suddenly there is, then it causes the skins to crack....I have no idea why that would be occuring in an aquaponic system.
If you haven't found an adequate explanation, I would suggest picking early. Tomatoes will ripen further on their own.
Just set them on your window sill.