Nenhuma explicação oficial AFAIK, mas esta teoria parece provável :
It’s also pleasant to see that Ayer and his costume team have realized that the actual mechanics of placing an augmented eye… device into the scope of a rifle could prove a little clunky, or redundant. As a result, it will be Smith’s left eye sporting the visual boost. Either that, or Smith is simply more dominant in one eye over the other (unlike Deathstroke, Deadshot isn’t considered to have one eye ‘missing,’ but either a cybernetically-enhanced eye, or both intact, depending on the writer).