If the registry edits don't work - the only alternative is to make / find a program that can click the popups to dismiss them.
I had to do something similar for garrysmod - a first person sandbox game/server.
When certain crashes happened, the restart couldnt happen until the process was completely terminated.
What you could do - potentially is Continuously check for Connectivity to your game servers port - when that connectivity fails - to a taskkill / process kill on nwserver.exe
A process kill / taskkill will kill the process and any associated prompts.