OK, so to answer the original statement of this topic - no, there is not performance difference in backup performance between VMware and Hyper-V. Likewise, all original ideas of why performance may be different (such as VM snapshot presence) were incorrect.
According to the logs, slow backup was caused by the fact that changed block tracking driver was not working, possibly because Hyper-V hosts required reboot after product update, or due to some 3rd party conflict, or something else. As logs show, drivers did start working couple of weeks later (without any changes on product side - likely, after host reboot). This particular case will be investigated further.
If you have similar issue, especially after product update - try rebooting your Hyper-V hosts first.