Not sure what you exactly mean.
Excluding the storage location from calculating the ABC indicators? Not possible based on the selection screen, except you do that by MRP area. You can anyway change the calculated CC indicator based on what ever reason manually.
Excluding a storage location from creating CC documents? No problem, storage location is a selection parameter and the multiple selection allows to exclude storage locations.
You have to decide if you can consider the quantity as accurate if you have a difference and did not look into a certain storage location. My most inventory differences where not real losses, just misplaced items, the loss in one location would equalize with a gain in another location