I regularly need to edit code that is in a very large source tree which is accessed remotely via NFS. When I first access an instance of this tree it is difficult to access files, presumably because ST3 is busy with the directory scan. Is there a way to suppress this scan, or at least control when it occurs?

Sublime Text 3 will scan the directory to find out about all the files, and it will then index the files, to enable Goto Symbol to work. If the latter part is causing issues, you can disable it with the index_files setting.