The best example of suffering from the bubble shields would be the sekhmet imgo. Awesome bomber, but it just has a damn huge profile. In the end you need to hit the hull anyway, but the huge shield is a setback when more than one enemies fire at you. While the one only needs to hit the shield from the distance and drain it, the closer one gets to the hull much easily. If the shield fits, both have to target precisely.
If you don't let the fighter through, you can't let through the support ship eaither. my guess is that the on-board computer shuts the quadrant down when something big approaches it.