Olá amigo,
Que eu saiba é apenas 1 database por instance. Da uma olhada no KB abaixo;
https://technet.microsoft.com/pt-br/library/cc708452(v=ws.10).aspx
"Each WSUS server requires its own database. If there are multiple WSUS servers in your environment, you must have multiple WSUS databases.
WSUS does not support storing multiple WSUS databases on a SQL Server instance."
Abraços