Technically speaking, imagine you're iterating over a million files, and some of them are 1000x slower than the others, it's not Backblaze's fault that things have gone this way. Avoiding files that are well-known network mount points is likely necessary for them to be reliable at what they do for local files.
It's important to recognize that these new OS-level filesystem hooks are slow and inefficient - the use case is opening one file and not 10,000 - and this means that things you might want to do (like recursive grep) are now unworkably slow if they don't fit in some warmed-up cache on your device.
To fix it, Backblaze would need a "cloud to cloud" backup that is optimized for that access pattern, or a checkbox (or detection system) for people who manage to keep a full local mirror in a place where regular files are fast. This is rapidly becoming a less common situation. I do, however, think that they should have informed people about the change.