I need to do more testing, but what I *hope* is the case is that they've been removed.
The reason I *hope* this is because the claim during 3.3's livestreams was that missions would contribute to who is winning the war. Of course, if winning CZs and handing in bonds also contribute, handing in a massacre mission would be double-dipping, which was the reason why not just massacre missions, but *all* missions had their effects removed.
Especially with the way CZs are now, it would be nice to have alternative ways of winning wars than slogging through crazy-high HP ships and churning through too many mats for reloads.
FWIW I didn't see any in the beta, nor in current live. If missions *don't* affect the outcome, it's a bit dumb that massacres got removed.