If you're on a 64-bit machine, the 32-bit RTEs will show up under HKLM\SOFTWARE\Wow6432Node\National Instruments\LabVIEW Run-Time\. If you're not on a 64-bit machine, there will be no HKLM\SOFTWARE\Wow6432Node.
This checks out my machine:
I would have no qualms about querying the registry, though I might go as far as testing the validity of the Path value.