Well, it also seems unlikely that no one around the time of the clone wars would go "Hey, these new republic warships look kind of familiar, where have I seen them before? Oh, that's right, the old sith empire used to use ships just like these".
Star Wars and the passage of time within the universe has always been weird...
It's not the passage of time that's weird. It's that none of them who write for Star Wars really care about continuity. I'd say even George Lucas doesn't care about continuity. All that matters to any of them is "Does it make money? Does it sound good?"
Everyone who writes for Star Wars wants to put their own spin on things, wants to make their mark, and they'll change anything and everything as they see fit/can get away with. TOR is no exception to this rule.