It depends.
If these directories are symlinks and the target is directly readable by your server i.e. these symlinks point to readable and browsable mount points you can select the Dereference Symlinks options in the options of the archiver engine to ignore the symlinks and treat them as real directories and files (follow the symlinks and back up the files under them). Please do note that restoring the site in this case will remove the symlinks and replace them with real folders.
If these directories are NOT symlinks but implemented with Apache code to read from external servers OR if their contents are either not readable or the contents of directories cannot be listed then no, you cannot back them up since PHP has no way of listing the files.
Another way to do that is to have one full site backup as is right now and one files only backup profile per directory you want to back up (e.g. images). You can use Akeeba Backup Professional's options to use a custom site root to point the site's root to the directory you want to back up. Restoring the site will NOT lose the symlinks but it involves restoring all backup archives, the full site backup in the site's root and each files only backup in the respective directory it is backing up.
Nicholas K. Dionysopoulos
Lead Developer and Director
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