The maximum number of hardpoints the ship can have is 1/50k tons, so the jumpship has a maximum of three. The original code was missing a zero and allowing 1/5k tons, but that was fixed in 0.45.3. So the removal of one from the jumpship is correct. A 400k ton warship should be able to have eight, so I can't see a reason for limiting you to two but since Hammer tried to reproduce it and couldn't my guess is that there's something wrong in the unit file.