I'm not sure if this is a bug, or the program working as designed, but it is an inconsistancy.
I have found that hyper-capable tugs cannot enter hyper speed when towing a non-hyper capable ship. However, these same tugs can enter hyper speed when towing a shipyard.
I can think of technobabble to explain either all hyper-speed towing is ok, or no hyper-speed towing of non-hyper-capable ships, but towing shipyards but not ships seems inexplicable.