I just found this on an older thread:
https://forums.ni.com/t5/LabVIEW/LabVIEW-as-a-Service-process-stays-in-memory-despite-finishing/m-p/...
It looks like you can define a .exe as a shutdown action and have your program respond to that (via tcp or w/e) (at least he says it works in srvstart)
