Yes they can go through the room without the Soldier being present.
The authority to perform walk-through or “health and welfare” inspections falls under the Commander’s inherent authority of maintaining good order and discipline of the unit. There is not a specific paragraph that authorizes this but it does fall under AR 600-20. Commanders have the inherent authority to ensure the Soldiers are living in a healthy environment and that the military quarters are maintained and clean.
What the Inspector Can and Cannot Do
This is always a touchy issue among Soldiers living in the barracks. The general rule is, yes, the Commander can authorize/order a walk-through of the barracks without the Soldiers present. However, the inspector can only observe what is in the open and cannot go through drawers, cupboards, closets, etc. Any contraband left in the open can be confiscated and used as evidence in any UCMJ or court martial proceedings. However, if the inspector opens a drawer and finds contraband inside, that evidence is not admissible as the inspector just went from an inspection to an unauthorized search.