Yes, using Custom Properties for the node or application and using this information as part of the alert criteria is likely the simplest/easiest way of handling this. I know Leon Adato has make extensive use of this approach. Alternatively, if you have an automation system you could programmatically unmanage these nodes or applications using the Orion SDK. Admittedly this it a bit more advanced, but if the process can be automated in some fashion then it might be worth the investment of time.
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