Eh, how is Bayonetta against foes she can't see? By which I don't mean stuff which is invisible to normal people and not her, but stuff which she cannot actually see? Because I like the Stone Mask.
I'd also wager that Link is sorta immune to time shananigans.
If she is able to percieve invisible angels in other dimensions, she will probably be able to notice link no matter how boring he is.
Link may have a noticeable strength advantage if he goes giant mode but Bayo is still powerful enough to damage link. If link does hit her she will take some serious damage and possibly knock her out. But she did come back from being completely flattened, toonforce style.
Speed wise she will be unable to blitz him but she is faster than he is and can walk on walls. She also has way more combos.