In VI properties you have the option to set the run-time position of the VI. Why not put hidden as a run-time position (or maybe call it state and position from now on)?
If you do not want your VI to have - or at least start with - a GUI you do not have the option to set the top VI to run with its window hidden from the start. Instead the closest solution you have today is to set the run-time position to minimized and then run an invoke node that sets the window to be hidden. Two of the most recents cases where I would have liked this is in a launcher app that just takes care of file associations (runs the main app and transfers the list of opened files to it...), and in a client app where some users want to disable the splash screen - which means that the splash screen should not be the top-VI but rather be called by a top-level VI that starts with its window hidden...
