The bind mounts will need to be remounted after the LUKS device is decrypted. Using LUKS has many issue with OMV because OMV expects drives to be accessible always. Unlocking on boot is my only suggestion.
Thanks for the info but I figured out what my problem was. The reason was the "share root filesystem" plugin by omv-extras. Since I removed this one the sftp server refuses connections when the encrypted device is not mounted and only accepts requests once its unlocked. Since I don't use "share root fs" atm it is not relevant to me, but is there a possibility for a fix in the future?