. . .During the ensuing battle, one of their missile destroyers surrendered, and now I'm trying to figure out how to disassemble it. Does the scrap task for a shipyard recover the components, or is there some other way to disassemble a captured vessel?
If it's a wreck, Salvage it. If it's intact, Disassemble will give you the components plus miscellaneous extra minerals. The components themselves can then be used, or disassembled for research, or salvaged/scrapped (I forget the exact term) for more minerals.
Also, what happened with the alien life pods I recovered? Were the aliens exterminated upon pick up, or are they now in holding cells somewhere, but I just can't figure out where?
They get transferred to the first colony population the host ship visits, where they get interrogated over time (disappearing form the game, but effectively being turned into intelligence points about their race).