Do SQL Server disabled databases cause any usage concerns?
I don't think you'll see much overhead except for system processes that enumerate databases for certain tasks. E.g. trace the server and expand the databases node in Management Studio - I bet you see a LOT more activity on the system when there are 50 active databases and 500 disabled databases compared to just 50 active databases.

Once a client has left, I would typically make a final backup of the database, mark the database as offline, wait 30 days in case they make any post-requests for data or reports, then drop the database once the backup is off-site (or whatever your "really backed up" status means).