Unfired jumpmissiles get targeted and destroyed from orbit by attacking ships during invasions- this seems to be an oversight, as they are not targeted during the "destroy enemy ships and defenses" mission and will be captured along with the planet if combat ships are ordered out of the system prior to an invasion. Jumpmissiles do not fire against ships or transports attacking their planet (since they aren't a normal planetary defense), so they get destroyed on the ground.
Jumpmissiles are a good counter to starships and a fair counter to jumpships for active players, but they can be negated instantly and permanently (no chance to recapture if the missiles are destroyed from orbit) by invading the citadel with a jumpfleet. An attacker can negate days or weeks of missile construction in a few minutes even if they don't even have enough troops to capture the citadel since the jumpmissiles get destroyed from space.
Agreed. For realisms sake, those missiles would be in underground bunkers away from orbital bombardment.