A family of System Center products that provide infrastructure monitoring, help ensure the predictable performance and availability of vital applications, and offer comprehensive monitoring for datacenters and cloud, both private and public.
Hello Bojan.
Just see this like any other SQL SP update or CU update. SCOM is just an app using one of the databases on your server.
If this is a sql clustyer you can use the clustered updates procedure and if this is just a single SQL server, it simply means SCOM will be down while you run this update. Pick a good moment for yourself.
SO go ahead :-)