As always, "it depends". Historically, you could only backup the VMs and then do a single file restore of the VM for individual files.
How large are the VMs?
How long is the retention?
What is the backup target/repo?

The advantage would be when you start with backuping the VMs you could start with the Community Edition if the features are sufficient. With the NAS backup, depending on the size of the file server, the license will quickly run out.

HI @dika,

As @MatzeB mentioned, it depends. What are your backup goals? If you needed to perform a recovery, would you want to recover the whole VM or only the files on it?

Do you have any specific RPOs and RTOs in mind?

Totaly agree with the “IT DEPENDS”

Nevertheless, I normally like to have a Full VM Backup, due to normally OS is not that heavy, easily deduplicated, and in worst case scenario you have a way to restore it entorely, not only data.

Please add some more info, as @dips and @MatzeB asked for, for better understanding.

cheers.

Are those VMs hosting the SMB file shares?  If they are hosting them I would back up the entire VM so you get the file share also.  If not then again need more information as asked above as it will depend.

I have a hard time coming up with an instance where backup up a files (via NAS license consumption) would be more efficient than backing up at the VM level.  The only exception would maybe be if you were backup up really really large datasets.  For instance, I have a client with a 100+TB file server, and that can be a bear to process, primarily for error checking, defragging backups, etc.  I suspect backing up as files might work better for this dataset, but it’s also going to be MUCH more expensive!