No, current implementation does not recursively read the directories in "template" folder.
One workaround is to create a set of soft links in the root directory.
I think there is/was some work around this area.
The solution I use is to keep all my ISOs on a Samba shared drive on my macpro, mounted R/O on proxmox host(s) so I can use them from anywhere. You could also use sshfs or symlink them from another local directory.
Script reads thru this directory sructure recursively and soft-symlinks them all flat with no subdirs in /var/lib/vz/template/iso , you should be able to adapt it pretty easily.