Basically for armoured and heavily shielded ship it should be no damage from handheld weapons at all. Just like you would need to shoot tank about forever with an assault rifle.I'm guessing you haven't tried this recently - it takes a lot of firepower to take out ships in ED now. More than just dropping an empty bottle, which seems enough to take out an SC ship ....
So shields could drain, but as engine is running and reloading shields that shoul put more energy to shields than small weapon can produce.