The Spirecrafts are just so damn specific and situational that it feels silly to buy most of them unless you have a very specific need.
Well, yea, they're going to be pretty specific: if they were mostly standard combatants for general purpose fighting it'd pretty quickly eclipse the need for a lot of the rest of your fleet and also not have a lot of variety within them. Golems are very rare, and the Fallen Spire ships (which if you want lots of general purpose fighting power in a super-weapon are the way to go) have a much more complex challenge associated with getting them and going on to win the game. So the spirecraft are generally utility for specific situations, though some of those are not as narrow as you might think. Implosion Artillery, for instance, is good against pretty much _anything_ with a ton of HP. How often are you facing AI stuff with tons of HP? That varies from game to game, but generally the variance is from "often" to "all the bleeping time"
And some of it really is quite niche, but when you've got a mining golem or a human colony rebels against the AI on some faraway part of the map those Jumpships are pretty useful.
the Spirecraft Scouts are so powerful they trivialize the scouting game for them
I dunno, the Mk4 Scout cuts it for me (BTW, is it intended that the resource costs of the thing are so low now? They were massively lowered when prices got linearized to the mark), Mk1-3 are good enough for finding the advanced factory and only then does looking for the AI homeworlds make any sense.
The m+c+e costs of the scouts don't really need to be that high, the main thing for the standard and starship scouts is their knowledge cost. If you spend the K to unlock mk4 of either of those then it's basically the "scout everything" button (over time) and that's ok. Though I seem to recall knowledge costs going down recently and I don't know if the mk4s of those were included in that. But yea, the balance of the scouting game is one of those where it's hard to get it right and keep it there; it often oscillates between "I can't get more than 2-3 hops out even with mkIIIs" and "I can scout the entire map with mkIIIs".