Inventory

I would like to idea of having something like an inventory where I can put unused stuff to.
The problem is that you sell stuff for the price for which you have bought it.

In my playthrough I gave a department 2 fully equipped operating theaters but I ended up using just one.
Instead of making a walled off room until I find use for it I would like the idea of putting it into an inventory.

In practice you could introduce containers/warehouses for rent which would cost a small amount per day,
depending on how many items you put away.

Make a separate room, like a warehouse and put all that stuff. That would be even more realistic then virtual inventory

This works as long as we are talking about 1-2 rooms worth of inventory. To change departments, wings or to even redesign the whole hospital, that is not a viable option and you then have to pay practically 150% for everything you sold and then bought again.

What I am unsure about are running costs for equipment and foundation. I'd like to mitigate that with my idea to mothball expensive equipment and suspend any running costs on them.

As far as I have been able to observe, there are no running costs. If you don't build anything, the only expenses for the day are wages, and possibly ambulance crews.