OK I figured out what my problem was. I couldn't access any applications because I was navigating to the Applications folder via my user rather than directly from the hard drive. In other words:
MacMini > Macintosh HD > Applications > <all applications are shown>
VS
MacMini > Macintosh HD > Users > <my user name> > Applications > <NO applications are shown>
So I was able to add the ScanSnap app to Full Disk Access and now ScanSnap is working again.
I'm still a n00b when it comes to OS X. I knew System 7 and 8 pretty darn well though! OS X is confusing to me. ?