Glad you like it.
I figured that making some of those things less prohibitively expensive would be popular, and at this stage would actually enhance balance rather than destroying it.
In terms of the starship costs... you're right, those were out of line a bit. And too varied by type of starship, in the main. I've normalized them more in the next version to work out to more like 80k combined of metal and crystal for them. The fleet starships are actually more like 64k, and the leeches are still higher than 80k, but in general stuff is clustered closer to the 80k total mark rather than the 120k total mark. I still think they were too cheap in the past, but I think you're also right that they've been too expensive more recently.
Also good point on the spacetime manipulators; I went ahead and reduced their cost to keep them useful.
In terms of armored warheads, those are sort of a "the first man to use these is the first man to run out of ideas" sort of situation, like the nukes. There are plenty of players that use a nuke or two per game, and that is just fine as far as I'm concerned; for the really advanced players that think they aren't to be used, that's also fine. Nukes are in a good place right now, and aren't meant to be used as part of every playstyle. I would say the same is true of the armored warheads, honestly: I don't think they are really targeted at folks like you.
The purpose of the armored warheads, as I see it, is to get to places that the lightning warheads can't for whatever reason, BUT that you still need to deliver massive firepower to. It's sort of a simpler alternative to a nuke (and cheaper) if there's just one keystone in an AI planet's defenses that you want to destroy without nuking the place. And, of course, these can hit mark V ships unlike a nuke, which is also good. Since lightning warheads are so fragile, these provide a counterpoint that are more costly in every since but which don't have that weakness. These have a particularly relevant purpose for anyone playing without the expansions (or without the relevant minor factions even if they do have the expansions), since they wouldn't have access to things like golems, spirecraft, etc, to accomplish the same sort of job without AIP.
In short, I see the armored warheads as still filling a somewhat obscure niche, but they're now actually useful again and are a tool that can pull players out of a bind. Particularly handy for the inexperienced players, which -- like the advanced warp sensor -- seems to me a valid niche to fill. If players eventually get skilled enough that they don't need crutches like that, then great. But having some transitional ships that players use while still learning the ropes more seems like a valid thing to do. Nukes sort of fall into that category as well, although I and a number of other advanced players definitely do use those on occasion, too.