Do SQL Server disabled databases cause any usage concerns? I have a SaaS e-commerce app. When clients stop using the service I disable their SQL Server Database and User Account rather than delete them.

Do these disabled databases cause any concerns related to stress on the server or SQL Server limitations on databases? For example is the any type of overhead just leaving them there? I have our backup tasks setup to not make backups for disabled databases.

I use SQL Server 2008 Web Edition.
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).