(1) Once in a blue moon, a lost/damaged civilian ship. The only sane reason for such to appear on the battlefield are damaged drives/systems. May be emitting distress signal. All diplomatic penalties for shooting /saving said ships in a zone of war apply. May frame enemy fleet by "causing" them to attack the ship.
(2) Expanding on the bounty system, you yourself can have a bounty on your head set by factions who don't wish overt hostility to the federation / etc. This may result in pirates stalking your fleet waiting for the right time to strike (after a tough battle, for example). You may wish to chase them out or bribe them off.
(3) Chance upon a derelict Voyager 2 equivalent space artifact. This has profound scientific implications of course, although with only some of the factions.
(4) Hunter-killer network guarding an orbiting body of interest. Perhaps guarding a neutral orbiting body of interest...
(5) A restaurant at the end of the universe.
(6) Self sufficient wandering space hippies.
(7) Of type 4 in your opening post, various utilities like large solar farms and space mirrors (oh the 7-years-bad-luck) are highly convenient for hiding behind. Captured-and-tethered asteroids/comets being prepared for mining by an orbital station (elsewhere). A good old mining operation that's been (or being) evacuated after hearing of your imminent arrival could be nice. Solar sails can be used to capture solar wind for H/He generation, although they're kinda low efficiency. Orbital elevators would be unlikely to be seen IMO as they'll likely be too heavily guarded to offer a mercenary a chance?
And then there are the more evil ones (in terms of destroying, that is), like magnetic field generators that protect a planet in question from being ravaged by the local star. Terraforming satellites (depending on the host species and their adaptability to the environment).
(
Do you already have Van Allen belts? Are you sure?
(9) The cookie monster.
(10) Wreckage of a space sausage delivery truck after an unfortunate interstellar highway accident. Not so good for vegans.
(11) Not just any sleeper station, but a deactivated von Neumann generator that assisted in a previous grey goo apocalypse. May irreversibly "cleanse" the local star system. I'd note that it's likely for a major faction to stop what they're doing and destroy these on first sight since it poses existential threat. One of those Voyager Omega Directives.
(12) One of the various space-surviving organisms you may wish to invent and populate the game with. Would it be space lichens growing on an otherwise innocent rock, omnivorous baceria, or a
giant jelly fish? Only the last one would require significant in-game art.
An asteroid studded with broccoli, on the other hand, might stretch the imagination for a good cause.
...you know, space is vast...