I agree with the thoughts expressed earlier, that Janeway (and the other Starfleet guys) probably knew. I suspect the reason Chakotay exhibits no knowledge of the Dominion has got more to do with him resigning his commission before Starfleet had first contact with the Jem'Hadar, so maybe he never even heard about the destruction of the Odyssey
. As a "private citizen" he likely lost most (if not all) of his Starfleet links, and he was effectively fighting his own skirmishes as a Maquis, so might have been "out of the loop" so to speak. Still no reason why Janeway couldn't have filled him in when she made him her XO, but hey-ho.