The default updatedb.mlocate cronjob takes hours due to large amount of lxc zfs datasets. If you want to disable zfs for this scan, just add zfs to PRUNEFS in /etc/updatedb.conf.
Large amount might refer to ZFS datasets in general. We do have a machine with ~20 LXC's which do have seperate datasets attached via mount points. The cron job is running for hours keeping the CPU busy. So to be correct, it depends on the amount of files rather than vms