I just did a quick test of this in a VM, and it looks like the LUKS plugin is currently incompatible with the USB backup plugin, no backup is run when the disk is unlocked.
There is, however, the potential for them to work - I edited the config for the USB backup plugin, and then it successfully ran when I unlocked the encrypted disk. So, yes, this would still interfere with process - you could not automatically backup just by plugging in as the disk would need to be decrypted, but after that step it is possible to have the backup run automatically.
I have submitted a bug report for this issue here: http://bugtracker.openmediavault.org/view.php?id=1470