I'm pretty sure that Spy Probe - Governance sends an alert to the planet owner based on the fact that I used one on a planet that I would have felt bad taking from the player if he was active and now he's upgraded the defenses and is guarding it only 12 hours later. The planet has only been scanned by the two of us and has never been attacked so I'm not sure why else that would happen other than by chance.

If it does send an alert the spy probe went from being just a waste of space to actually being harmful to use.

as far as i know it doesn't send out an alert

99% sure it works just like the other spy probes, meaning there is no way of knowing if one was used or who used it, maybe he just saw that his planet was scanned by other ships and wanted to protect it