The NPC ships carry Caldari Navy tags.
While I can understand the whole "militia act designed to prevent direct confrontation", this did not stop the State from auctioning off development rights to the territories, landing troops on the planets, installing new regimes, enforcing a communications blockade etc.
This is war, it's not a case of trying to demonize the State, or the big bad Federation. Federation Navy ships occupy Nisuwa right now, for example. And according to the Caldari epic arc, the Federation Navy maintains a forward presence in Black Rise, detention centers with raped women etc etc.
It's direct conflict that doesn't happen, and that CONCORD doesn't allow. The militias clean out an area of enemy navy presence, and their navy moves in. Take "To Live in Peace" which infers that the Federation and Caldari have continued to be fighting each other even when the first war passed.