Not a bonus ship type, but would you consider Scout Starships for nomination? They're just so...so...pointless.
Not quite pointless.
1. Much more durable than fleet scouts
2. Not only are immune to sniper shots, but can counter them as well
3. Can decloak stuff
1. Lack cloak boosting, so its trickier to take advantage of their better durability for scouting (thankfully, cloak boosters prefer to boost starships over fleetships, so any fleet scouts you bring along will try to keep the scout starships cloaked first)
2. Them not being considered military ships messes with you trying to use them in a fleet. There have been several suggestions about how to fix that though.
3. Higher marks don't really give you much more than better durability and I think better speed. (Except for Mk. IV, which is immune to tachyon decloaking) There has been some suggestions about fixing this as well.
4. Their secondary effects are not guaranteed to be useful in all games. It's usefulness plummets dramatically if the AI unlock neither a fleet ship with infinite range (which is considered a sniper shot by the game) nor a fleet ship with cloaking.
5. Decloaking range is so short, they will probably be in firing range of the cloaked ship before they can decloak it
6. Have an oddly long build time