General answer:
You would not "delete" the files, but rather replace them... sort of.
.vp files are sort of like .zip files, except they are not compressed.
However, FreeSpace first looks for the files in the actual FreeSpace2 directory, then in the .vp file.
So, say the file ships.tbl :
there is one in the actual FS2 directory: \freespace2\data\tables\ships.tbl
there is one in the .vp FS2 directory: \freespace2\root_fs2.vp\data\tables\ships.tbl
The file in the actual directory overrides the file in the .vp directory.
Also, if more than one .vp has the same file, the .vp with the higher filename wins.
For example, if you wanted to have a .vp with some files overriding some of the files in root_fs2.vp, you could make a new one called a_root_fs2.vp
I do believe that it is possible to disable a file (like deleting it) by placing a blank file (create a blank notepad document) of the same name in either the actual FS2 directory, or in a highter-named .vp