Not sure if there was something irregular about my original installation, but the music on hold files were under /var/lib/asterisk/mohmp3. When upgrading to 2.9, the system started to look for files in /var/lib/asterisk/moh. As a result my music on hold disappeared. After copying the directories and files from the original directory to /var/lib/asterisk/moh and doing a reload, it was not sufficient to create the categories in musiconhold_additional.conf. I had to create a new category and reload freepbx before the existing categories started to show up.
If my setup was irregular, then this can be closed since the problem is solved for me. But thought i would point it out just in case it's going to be a general issue on upgrading.