I think to reduce the overpoweredness of ship labs, the following should take place once the tech is researched:

1) 1st level of tech should give weapons labs, 2nd level should give imperial labs.

2) On each tech level research, the following would also occur:

a ) Labs of that type would be disabled, to have no effect on tech tree. This should be a permanent, uncounterable, undisablable effect.

b ) Labs would be auto-scuttled. This scuttling would be unstoppable. Player gets resource payback normally from this scuttling.

c ) No more labs of that type can be constructed.

This IMO would mitigate, perhaps solve the OP'dness of ship labs. You are basically trading the physical labs for ship ones, and forfeiting the construcion of planet labs altogether.