@ Antartic: I did thew same raiding strategy*, and out of curiosity, saved the game, set the speed to fastest and let many days go by, and still didn't see any respawning of ships (before I destroyed the ship-building structure, that is). You mentioned they "take a while" to respawn, did you see them respawn at all eventually? If so, at what difficulty level?
* = Only I found 3 Annihilators packing Heavy Disruptor Beams and Disruptor launchers, with a double load of X-Com targetting systems and large shields each, did the job, at the second-to-last difficulty level.
@ Sy: I haven't tried the hoverbike thing you suggested (I always go for the state-of-the-art equipment myself :P), so I'll take your word for it, but it might become costly due to losing a couple of units each time (and, more importantly, the weapons they pack). Retaliators and then Annihilators are the thing to go, both because they are the only ones capable of packing the heavier weapons and equipment (Annihilator specifically is the only one that can fit a heavy disruptor beam) and because they are the only (fighting) units able to go to the Alien Dimention, and that's where you're bound to take the fighting to.
When you figure out the research tree, try to build only 1, at most 2, Retaliators as you rush to complete research on the Annihilator: one doesn't quite make the other obsolete, but almost. :P