I haven't seen it in the shop, but it can be found.
SPOILER: Visit "border" systems at the north-east edge of the map. Beyond Blockade Point Something - right now I don't remember which one - occasionally you'll find jumppoints to uncharted Kilrathi systems. One of them contains an asteroid that can be docked.
I believe that you have to finish Soren's mission branch of the side campaign to be able to get the Cloaking Device, but I don't know that for a fact. And yeah, it's a really cool piece of equipment. Makes intersystem travel a LOT safer if you aren't looking for a fight.