What has MIRO transaction to do with storage locations?
you should never delete anything from customizing if it was/is in use, as this creates certainly unwanted effects.
you have materials with this storage location, you have POs, production orders, movements with this storage location. So it is in use. On after you have archived all this data, then you can delete a location from IMG.
Very often SAP validates the existence when you display old documents and you may get dumps in that case if you have deleted customizing. you may not be able to archive the material master with this location in future if the location was deleted from customizing.
Better you restrict its usage with authorization settings. (dont understand anyway why someone should use a storage location in SAP that does physically not exist )