I am new to the forum, but an old fighter jock whose played through the whole series since release. But back to the slave ships . . .
The key here is to inspect the slave ships and disable them as quickly as possible. All I can say is that the shuttles are flying in groups of 3. In each triplet there is one slave ship. After a few passes you will probably catch the pattern, that they are flying in.
As for speed in dissabling the craft? The absoute fastest way to get those shields down and the craft dissabled it to launch _one_ torpedo at it and then finish it off with ion cannons. The torp will strip the shields and leave the hull around 95%. All that is left is a few shots from the ion cannons. With some practice, you can head to the lead ship and then slide down the convoy inspecting and taking out the slave ships in one pass.