I think the whole idea of a “Self-Destruct Mechanism” on a space ship has been very badly thought out and executed. One of the high points of the TV movie Something is Out There comes when the Earth guy asks the alien woman why she doesn’t just use the Self-Destruct to blow up the ship and get rid of the Monster, and she asks “What self-destruct mechanism? If you had a ship, would you put one on it?” Which sums it up pretty well.
I can see it making sense in some situations – really big ships that are expected to go into orbit and which would be in a position to wreak havoc if they fell, reaching thye ground in big pieces despite atmospheric friction, and which might not have the best control and guidance around. The ore freighter in the original Alien is actually a pretty good candidate. Various small military ships might want them, too. But there’s not a lot of point to putting one on, say, the Enterprise (despite “The Corbomite Maneuver” – and that was a hoax, anyway). We saw in ST III that the Enterprise would burn up on its way in (although her successor under Picard evidently wouldn’t). And do we put such devices on our own ships and planes today?
A bomb big enough to take out a big ship is a terrorist device waiting to happen, a grave temptation to the crew, and a pain in the neck to keep in guaranteed workling order. (A lot of places I’ve worked had trouble keeping the fire extinguishers fully charged. If we ever had to use the Self-Destruct to blow up a building, I guasrantee it wouldn’t have worked). The accountants would bitch about how much usable capital was tied up in a device that would probably never be used.
About the only moviwe I’ve seen where such a Self-Desttruct Device was used properly was Robinson Crusoe on Mars, where the Mars expedition had one on the ship, and it was used (as the original RC used his) to get rid of a device that indicated his presence to unwelcome visitors. Also the only time it wasn’t played up and used at the climax of the film, but dispatched in a businesslike fashion.