Do you care about possible Spectre- and Meltdown-like CPU vulnerabilities? Do you use your Qubes OS normally while backing it up or do you Pause All VMs for Secure Operation?
I don’t see how pausing a VM protects the data in it from side-channel attacks. Paused = in RAM. Even after a shut down, some data still remains cached, unless there is some explicit mechanism which zeroes/shreds/otherwise-overwrites the content of the memory cells used by the VM.