Well, CBS did block the Enterprise-J's appearance in STO. They ain't likely to allow Tier 5 variants of 23rd century ships either for basically the same reasons. But other than that... really? Any five minute trip to ESD will blast your screen with TOS-era Connies flying shotgun to Sovereigns and every player character gets Wrath of Khan uniforms for free. If they're catering to canon nuts, they're doing a pretty lousy job of it.
I think the few publicly disclosed veto actions CBS has made so far are perfectly understandable and the game is better for it. More than that, no one here works at Cryptic Studios, so we're not privy to the developer/rights-holder relationship going on. All we can do is speculate about what the suits are up to and, frankly, I'd rather spend that energy elsewhere. Such as playing the game.