Thanks for contacting AppDynamics. Please let us know which agent version is installed in your servers. The commandlet is looking for the registry key
HKLM:\Software\Microsoft\Windows\CurrentVersion\Uninstall with a Displayname value equals to AppDynamics .Net Agent. If it can't find that entry, 0.0.0.0 is returned, which means no agent is installed.
So, in a machine where no agent is installed, the response you got is expected. However, in the machine where the agent is installed, these registry entries must be present. So, we have to understand why those registry entries are not created. If the registry entries are corrupt, they can be fixed by launching the Appdynamics configuration wizard (from start menu).
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