But cloaked missiles should not be a side note in the Dominion War if they existed.
Why not? They would have been a side note to Sisko or Worf, who wouldn't be involved in the selection of targets or the planning of the attacks. That's an entirely different department altogether.
And DS9 isn't a TV show about a "submarine"...
It's a TV show about a space station and the starships assigned to her, thus no need to mention what the land armies -- the people most likely to use those kinds of weapons -- are up to. Conversely, no mention of submarine warfare is ever made in Saving Private Ryan or Band of Brothers, much the way Sisko and Martok and Worf never mention the Klingon artillery battalions that would have been responsible for the deployment of warp-powered cloak-capable cruise missiles.
Which shouldn't be surprising, really. If they hadn't filmed "The Siege of AR-558" we'd still be debating whether or not ground combat even occurred in the Dominion War.