It would help if you could give some examples of applications that cannot see the drive, but I could bet these are the ones that are not integrated with Gnome.
In any case, you should try to see whether your NAS has been mounted with gvfs (this should be the case if you mount it from Nautilus). Go to your home directory, and change to a hidden directory called
.gvfs/. Your volumes should be mounted here, and all the applications that cannot find it like Nautilus does should be able to navigate to these mount points.
You see, what happens is this: in Unix/Linux, any shares / drives / etc. are mounted within the normal filesystem hierarchy. Nautilus and a couple of other applications additionally show these mounts on the left side of the file selection, but this is an additional behavior. If you can access the shares with Nautilus, then they are mounted somewhere, and any application, even if it only understand local filesystem, should be able to find it.