Have 'Automatically Empty Trash' Skip Libraries with Unavailable Folders

Plex is already doing that.
If the file share or drive is not accessible at all, Plex considers it as “temporarily unavailable” and doesn’t trash the media.

However, this safety mechanism is cancelled if you don’t point Plex directly to a file share or traditional drive.
If you for instance use “directory junctions” on Windows to mount a whole different drive to what looks like a simple subfolder of your main drive, then Plex cannot tell the difference between a lost drive or a genuinely empty folder.

Example:

D:\Movies <- Plex library points here
   \Movies 1\ <-- regular subfolder, containing movies
   \Movies 2\ <-- additional hard drive is mounted here

In the above case, Plex simply assumes that the subfolder Movies 2 is empty, if the additional hard drive which is mounted there gets out of order.
Because the hard drive D: (where the library points at) continues to be available.