How about this method:
User can define a filter on the directory tree, just like the filter for normal file pane. Then TC scan the drive to build a special tree of items should be filtered, merge this tree with the current full tree to display the filtered view of directory tree. I think the merge of two tree should be easy and fast. Of course the special scan could take some time but that is natural.
This way the treeinfo file is left untouched, so old version TC can work as before, because the special tree info file is not recognized by old version TC.
With the filter, user can hide the hidden directories. For me, I'd like to hide some top level system folder too.
Besides, if you ever used a new software called Everything search,
http://www.voidtools.com/
you will find it can update any changes in your drive in seconds, vastly faster than any software before. It's because it utilized NTFS journal, so it can update lots of changes really fast. I'm not sure if this method can help TC too.