I was able to warp a tiny ship armed with an IC2 nuke through ARS shields and blow up another ship. Not sure if you can, but this should be fixed. Maybe allow it through a modulation block or something. To go along with the Star Trek/Star Wars lore you are trying to emulate, this should be fixed. Its only lore friendly if its from hyperspace per the new Star Wars movie, not in regular space.
Using a modulation block, you could go through shields, if you have the right frequency. I cant think of any examples of warping through shields besides TFA.
...just a thought