Getting back to the original question, the Bondage and Laatex Fetish Masks are both new. How new I'm not exactly sure, certainly within the last couple patches. It looks like they were automatic additions since I know I didn't fight any new enemies and see any messages about Nova upgrades. I, too, wear her exclusively.
As for the rest of the upgrades, they're pretty straightforward IMO. They're all listed in the wiki. Granted, they'd be pretty hard to come by naturally during the course of the game, but the devs and writers have historically been great about including roadmaps for stuff like this either in the wiki (eventually) or in the change logs.
Story-wise, sentient, friendly grey goo is new to both of you. Upon creation, she doesn't yet know all of her capabilities and neither do you. Having her to turn into a suit that looks like a crotchless, assless, breastless Mechadodzilla that can fly and shit rainbow lasers from day one is not good story telling.
My question about the GGA is why have an option to add an emblem to the armor and why does it disappear when in swim suit form? It sounds like future content is planned where you need the GGA with a specific emblem displayed in order to go undercover in some corporation's headquarters.
Of course, I'm probably way off base and nothing of the sort was ever planned. It's just odd, is all.