I'm pretty sure that's not why he was angry.
Also, if S31 confiscated it, shouldn't it have been a huge shock when they found it was used? Wouldn't the idea that technology is confiscated and not allowed to be used be a huge red flag?
This post just makes me ponder what the heck Starfleet/the Federation did with all that technology that our heroes have found over the years, from TOS to Voyager. Sure, the novels always say that they're tucked away, but that's not really canon. Surely there are results from the Dyson Sphere expedition force, or the Planet Killer being reverse-engineered. Voyager bought super-powerful torpedoes from an alien vendor, but the only time we ever saw it was the test fire.
The TNG crew appropriating nanite technology with the possibility of using them against the Borg is one of the few times I can think of where previously found technologies and discoveries were even mentioned again, as well as the Iconian gateways returning in DS9.
Of course, the simplest answer is that the writers had other ideas, and that the episodes with those technologies were rarely ever meant to have follow-ups. But still, even just between Kirk and Picard, Starfleet should have quite a collection.