Wasn't quite sure how to title this. But here's my issue.

While playing, I used Hit and Run with Chewie to kill two Storm Troopers in an Imperial Loyal System (Saleucami). Does this system loose the Loyalty AND Subjugation? What even happens in that instance?

Loyalty is completely independent of troops.

You can have a loyal system with no units present.

Subjugation marker is there for systems that are not loyal to the empire (either rebel loyal, or neutral). Subjugation only lasts while the Imperials have troops there; once they're gone, the system goes back to previous ownership.

For your specific example, assuming the Empire only had 2 troopers there: both units are destroyed via the mission, the empire then has no ground presence, but the system remains loyal to the empire.

Couldn't have said it better myself. Don't put subjugation markers on Imperial loyal systems. They get the full resources regardless of military presence. Though having your rebels there DOES cause the system to be blockaded, which is a whole other ball of wax.