@BuZz ... Can't believe I hadn't thought of that before. SHAME on me :-(
Thanks so much for your patience, this obviously did the trick. What I did is put that command in /opt/retropie/configs/all/autostart.sh, before emulationstation is called (otherwise the games didn't show up in ES because the USB wasn't yet properly mounted). It's still unclear to me why games can be accessed via symlink in ES, but the parser cannot access them. Oh well, the workaround works, and I hope future Googlers will find it easily. Phew!