Well, unless you're going to deactivate the stateroom and remove it from the aircon, the plumbing, the gravity and the power grid (and feel free to do so with unused staterooms to reduce expenses!), there's some running costs right there.
Power is just power and that is already accounted for in fuel costs. The cost is tens of credits even if using refined fuel (which is only needed for jump engines). If you don't use a tap it doesn't use water, there is no need to disconnect it. A stateroom full of air is a reservoir. If you don't use it, it doesn't get consumed. Air will be much more carefully managed on a space ship than on a terrestrial vessel, the ability to isolate the air supply to a staterooms would seem to be a basic function as both a fire/smoke control and breaching/contamination protection.
Given the tight budget ships are run on it seems incomprehensible that you wouldn't be monitoring and controlling usage of consumables very carefully.
I've always taken it to just be the cost of the occupied space in total. There's no base life support cost for the bridge or the engineering compartment, even though those also have gravity, and air and power and possibly plumbing.
That would explain the Cr1000 per person. It is irrelevant whether they are in their stateroom or on the bridge, they consume air (which presumably needs filters or bottled oxygen or something), water and food. I am ok with that, but I am not sure what the extra costs for staterooms are. If high passengers has a higher life support cost (representing fine foods and drink and possibly special scented air) I would understand, but they get the same as everyone else.
It is not universally applied either. Acceleration seats don't factor in life support, they are supposed to be for short occupation, but that is still up to 24 hours. The Lifeboat in the Small Craft Catalogue has 20 of them (plus 10 low berths). It is designed for "keeping the people on board alive for months if need be." It has 32 weeks of fuel to run the power plant, but no money or space allocated for food, water or packaged air. Now you can survive without food for months, water less so and without air you will be dead in short order. I am sure there are other examples if you care to look. Interestingly the Life Support module from that book indicates that food is not a component of life support (I tended to assume that life support meant air and heat).
Barracks cost twice as much per DTon as a Stateroom but you would expect the facilities to be even more spartan there as it is classed as Basic at best. High and Luxury staterooms have higher per room costs, which could be explained away as higher quality foods etc. but that cost is not applied to high passengers in normal staterooms. The Brig can support 12 people for only an extra KCr1 per month.
I can just handwave it off, but I know my players are going to ask about cutting corners at some point, and I'd like to have something better than "it's the rules".