The background information Cryptic had to justify the time ships stated that the Tholian's ripped out most of the future technology. I'd think a cloaking device 400+ more years advanced than any current KDF technology would be the first to go.
An actual cloak on the Krenn would mean it can fire while cloaked, completely undetectable with 25th Century technology, unaffected by enemy weapon's fire, and can give those same benefits to anyone on their team. Since this is a MMO and not a single player game, then certain restrictions have to be put on it to make things balanced.
Future sensors are probably so sophisticated that they can detect any gravitational disturbance including small ones like starships.
Since even the best cloak can not hide the ships gravity well it would be pointless to use them in the future.
In fact the only cloak in existence are naturally occuring black holes BECAUSE they have incredibly strong gravity wells and create gravitational lensing which makes them detectable indirectly.
The only way to avoid this is to not interact with the rest of the universe. Even if a ship could do that the non interaction part would be a 2-way street which would blind it's own sensors and weapon capabilities.
Closed Warp bubbles have been known to do this in TNG's "Remember Me" and look how that turned out.