It's because Backup solutions take snapshot of the powered on VM, then take backup of the VM as all the virtual disks are having their state preserved and new changes are being committed in delta files while backup job is going on, at the end of that backup job, snapshot will be deleted and VM continue to work.
In the blog you are referring , Cormac Hogan is not telling that backup is not important for the data residing on independent virtual disks, he is just mentioning that they are not included as it is when you run a backup job, because independent virtual disks don't participate in snapshots so in a way they are not being backed up as Let's say guest OS within the VM is still doing read/write with independent disks so backup software is not able to get the backup of it in consistent state.
now we have two possible solutions to take a backup of this, either I take VM offline and take a backup of that VM, or I install backup agent at guest os level and that way I take a backup of data residing in independent disk. as you have mentioned in the post, that you have many independent virtual disks which you take backup of regularly so I believe you are taking one of the two mentioned approaches.
Please refer following URLs for some more light on the subject
VMware KB: Taking a snapshot fails with the error: Failed to take a memory snapshot, since the virtual machine is co…
Acronis Backup & Recovery 11.5 Help
https://www.vmware.com/support/vdr/doc/vdp_600_releasenotes.html