I noticed after putting the borg set whenever I cloak and then decloaked my B'rel refit no longer showing any contrail at all. All the special effects from the borg set on the ship exterior seems to be missing too. The parts are still showing but there is no longer the glowing effects or any other effects aside from the borg structure itself.
Now if this is a bug as what I suspect it is I'm not complaining as it is beneficial for me flying the B'rel without any contrail as it made me more difficult to track visually in space.