I'm using OMV5 + Luks + SnapRaid + Union/MergerFS and also had a problem of rebooting into emergency mode.
I hava managed to workaround this issue by adding "noauto" option in mergerfs entry in /etc/fstab. This disables the automatic mounting of mergerfs partition at boot (which cannot possibly succeed without unlocking Luks first) and causes OMV5 to reboot normally with GUI available. Then I unlock encrypted drives manually and, after that manually mount the mergerfs partition
After that, shared folders immediately become available via SMB. Also, branches tab in UnionFS plugin gets updated automatically. I didn't test NFS, though. I don't mind doing manual actions after reboot because typing in Luks passphrase manually is required anyway. It would be nice if there was "mount UnionFS" button in GUI, though...