Facial recognition systems can be (and are) trained to not be fooled by things like facial hair, hair changing, eyeglasses and sunglasses, hats, etc. Although it can obscure your features for sure.
If someone does something really odd to try to avoid the facial recognition (I've people posting things like making your hair non-symmetrical, or just avoiding the camera in the first place) then they just train on those things too. And that person gets flagged as being really suspicious. And things like full face masks are banned in some places already.
This will have two effects.
People who are truly suspicious for nefarious reasons will gradually stop being so.
On the other hand, many will be incorrectly flagged as suspicious and harassed without reason.
The trick is to strike a fair balance between the two. But who decides what's fair?
This is simply the same trend as ATMs replacing (some) bank tellers many years ago.
Will it be easier to perform and abuse mass surveillance? Sure. Will people with something important to hide still wear disguises? I'd bet yes.
My stance is that we can't fight progress, but we can start fighting the people bent on abusing the powers that progress bring. Identifying them is another issue (perhaps some form of facial recognition? :)