phpMyAdmin was working fine with that symlink on a test site, but for other reasons I've installed again Linux and ISPConfig 3 in the same VPS, this time on Debian 5.0 instead of Ubuntu 10.04 LTS, since Debian seems to be the most supported Linux distribution for ISPConfig. I've followed The Perfect Server - Debian Lenny (Debian 5.0) [ISPConfig 3]
This time, phpMyAdmin is working correctly at example.com/phpmyadmin after installing ISPConfig 3, with no need for that symlink, etc. I'm not sure why fixing it was necessary the first time, perhaps I did some mistake during the installation.
There is also a tutorial to Protect phpMyAdmin On An ISPConfig 3 Server (Debian)
, by a new URL and an additional password request.