Readers know that Hooper can't stand the sight of his own reflection with the veil hanging before his face. He is so averse to himself that he avoids mirrors and even calm, reflective water.
In truth, his own antipathy to the veil was known to be so great, that he never willingly passed before a mirror, nor stooped to drink at a still fountain, lest, in its peaceful bosom, he should be affrighted by himself.
What is not explained to readers and is, therefore, open to reader interpretation is exactly why Hooper is so frightened by his own image. It is possible that he is scared of the physical image of a person wearing a scary black mask. This might make a lot of sense if he was a 7 year old child or he came across someone that he didn't know wearing the veil; however, he is an adult. He knows that he is wearing the veil, and he likely has a pretty good idea of what his image looks like. I think he is averse to seeing his own reflection, because it makes him think of all of the reasons he's wearing the veil in the first place. The veil is symbolic of hidden sin, and when Hooper sees himself, he is viscerally reminded of all of his hidden sins. Running into the darkness is his way of running from those sins as well as eliminating any chance to see his reflection. If there is no light present, then he can't see anything being reflected.