Some apps, though not all, provide config settings that let me redefine the default directories. Please let LabVIEW provide such settings in a convenient way, such as via the Tools-->Options menu.
And just to throw another option into the mix, you could try letting the user define custom logical directories, although this could get ugly fast (e.g. what happens if you try to open the directory on a computer which doesn't have it configured. Also, the directories proposed here should probably be enough to cover the relevant use cases).