Believe it or not, the Scripts folder is only there for extra custom scripts that may be included with the various Tables, depending on a Table Author's preferences.
The .vbs script files for VPinMame have never been assigned to the Scripts folder, only the Tables folder. This is because the Tables folder is where VPinMame looks for the .vbs script files based on how VPinMame is written or based on the settings.
Not sure if the VPinMame .vpt Scripts PATH can be changed or not. I've never thought to try it.
Now about the custom scripts by authors. These scripts in practice can be placed in any folder on the hard drive, as long as the Table.vpt script has the correct PATH to find it. A PATH is the address (the directions to find the location) of a file, script, etc. on a hard drive.
So the Scripts folder was included long ago to make it easy for users to know where to place any additional custom author scripts that are found in the download.zip for a table, with the understanding that the authors could write the PATH to the Scripts folder (written in the NameOfTable.vpt internal script) to enable the Visual Pinball program to find and use their custom scripts when playing the Table, so that everything would be easy for the users.
But, with the .vbs scripts by design placed in the Tables folder, and the reality of most users simply unzipping the Table.zip contents to the Tables folder without checking the contents, most authors then decided to simply put their custom scripts in the Tables folder also, and write the PATH to it.
Because most new users simply unzip the Table.zip contents to the Tables folder without checking the contents, it turns out to be the easiest choice.
Years ago when most users were on slow dial-up Internet service, authors would sometimes write the internal script for their Table as an external file.
This was done so that, if there was a bug in the script, the user only needed to download the smaller replacement script instead of the much larger whole table.vpt file.
This was one use for the Scripts folder, but as stated, a script can be placed anywhere, as long as the PATH (in the internal Table.vpt file) points to its correct location on the hard drive.
I didn't know the history either. Thanks Sleepy. The reason some table developers use vbs files today is to easily apply the same script to many tables. Of course, you have to add code to the table to run the vbs. It can turn into a bit of a mess if the author does not have has good version control.