So I know from trying them out that "Leech" guns and missiles seem to simply disable enemy ships, but what good does that do? It's a lot harder to disable enemy ships than blow them up, and it doesn't seem like there's any point to do doing that. It's not like you can then recover the ship and use it or something like that, you know?

Anyone know what's their intended purpose?

I think it's a moral choice really. When I played the game back in the day I didn't mind killing Kilrathi but it bothered me to be shooting fellow confed pilots who may have just been caught up in the whole conspiracy. Leech missiles was a nice alternative (as are the leech guns available on some fighters). However it was never implemented fully as often leeching enemies means that the next wave will not spawn or that you can't autopilot meaning you still have to kill them after disabling them... and that just felt even more wrong! Shooting down disabled ships?

Anyway, I have no idea if this was originally going to affect your squadmate's morale or not.

There is even an alternate cutscene with Seether and Paulsen escaping from a disabled Lexington if you leech and not destroy it. But never found if it has any effect on game, especially the ending.

Also in a number of missions you have to capture transports or fighters and leech them first. Leech missiles are effective against both fighters and capships, when flying a ordinary fighter against capships Leechs are often a faster way to neutralize them.

Really? I thought they escape the Lexington even if you destroy it.

They always escape, but one time you see the Lexington's burning wreck and otherwise an intact carrier with flickering lights. The cutcenes are SC_1200A.vob and SC_1200b.vob