I'll make this point in regards to the Mirror Universe portrayed in DS9:
There's no reason to believe that the Mirror Universe shown there is the exact same one that Kirk visited and set things in motion in. Despite what they say on DS9.
Think about the episode with Worf popping from reality to reality in TNG, they've shown already bajillions of universes based off the Trek universe that we were familiar with in that episode.. what makes it less likely that there are similar versions of the Mirror Universe that we first saw in TOS.
I like to think that the Mirror Universe portrayed in DS9 is a similar Mirror to the horribly flawed Berman-ized version of the standard Trek universe that we saw in late TNG, DS9, Voyager and Enterprise. And that it is *not* the DS9-era version of the Universe that Kirk visited in TOS. But nothing is officially canon after Rodenberry left TNG anyways... just that the Berman-bastardized versions of Trek is all we see now.
Ruling out Mirror Universe ships simply because "The Terran Empire doesn't exist anymore because we didn't see it in DS9" is like saying that humans *will* someday evolve into the reptillian thingies we saw Janeway and Paris turn into on Voyager. It was stated as fact in that episode as well, but personally I think the writers meant to say "devolve" past a primate stage without passing go. Or that you can have the Borg inject Phlox in "Enterprise" and not only is he running around for days and days (from the looks of it) with nanoprobes Borgifying him, but that he's able to wipe out the nanoprobes that had eluded a cure from superior technology 200 years later. Oh yeah, and they can easily clean Borg components out of Enterprise at the same time period. Uh-huh.. welcome to Berman Trek.
I look at it this way. Roddenberry said that the Empire would last probably 200 years past TOS, and I believe him because he created the Trek universe. So it does.
But your mileage may vary of course..