Virtual thoughts are not good for me, because there is no fulltext index of the files possible. Why?
Not being able to index files in virtual folders is to me a good idea, as this keeps them separate from the rest of the files which are "associated with" your Brain. I see virtual folders as simply "windows" out of your Brain to selected groups of the files on your hard drive. Thus, if you wish, you can work entirely within PB, instead of making it just one more open application among many already open, and link a thought to a number of other files, maybe even applications, where there is some connection.
For example, (in Windows) you could set up a folder on your hard drive containing nothing but shortcuts to your text editors (this could be a subfolder of the Start menu - let's name it Editors). Then you might also have a Thought named Text editors so you could make Editors a virtual thought (virtual folder) of Text editors.
Anyway, what's to stop you from putting all your .doc files in one folder (let's call it C:\mydocs), linking a shortcut to each document to its relevant thought as a file attachment, AND ALSO making mydocs a virtual folder to another thought? In this way you can have your cake and eat it. You can inspect which .doc files are present by looking inside this virtual folder, and since each is linked separately to a thought, they are indexed too.
If you want to link a large number of external files to a particular thought, creating a virtual folder for it as well as stacking all their icons on top of one another might make it easier for you to select the document you want to open. Just my 2 cents worth.