In late game, resources are still a very valuable commodity, as they are what allows you to rebuild your fleet. I think it's a much better idea to be able to rebuild your fleet a few dozen times as opposed to making a superfortress.
You're also much more likely to build a bunch of black hole generators, zenith reactors, and radar jammers as they have a niche that is unfilled by knowledge unlocks. Why spend 18 million of both resources to build something that in actuality is just a slightly better version of something you can already easily get? Why not make black hole generators to seal chokepoints? Why not build a bunch of MkII radar jammers to inhibit the enemy fleet?
Besides, in order to even support such a structure, you'd need upwards of 20 planets and many, many spire habitation centers in order to even build it.
So, yeah. Not worth it at all.
Ion cannons are useless as of now, they scrap for very little and don't make much of an impact in battles when you control it. I agree, this probably needs a buff, but not with firing rate, as it makes them so much more deadlier when the player is engaging the world.
Counterspy is too expensive for its utility; it hits only cloaked units and is very fragile. Unless you're very self-conscious about having red 1's and 2's on your planets, it's not worth it at all. Even then, you need only to unlock decloakers.
Orbital mass drivers...well, yeah, they need a buff. Too ineffective overall.