reading through this im noticing two different types of stealth tech being talked about. We have Visual Stealth designed to keep you from being seen by the nkaed eve, and electronic stealth designed to keep you from being seen by radar and sensors.
I believe that the two should be seperate in a sense, for instance if you build a ship that has a cloaking device, then the ability to be seen on scanners for things like power use, engine plumes, and radio trx etc should be seperated. Likewise if your ship is masked for sensor stealth to where sensors on other ships not operated by you or your clan can not detect you, or it is more difficult to detect you, then it should be seperated from the visual side of it.
I am also a fan of covert ops, so maybe make it possible to mask from both, but make it very very expensive. Real life for instance, the B-2 Spirit stealth bomber which costs nearly 3.2 billion vs a normal bomber like the B-52 costing 36 million. In game make the modules extremely expensive and there still needs to be an advanced equally expensive way to counter it.
Long story short i believe that Covert ops setups are a valuable part of the game as long as they are implemented well, personally i think they should be hard to get and even harder to afford.