It shouldn't. A civil PE is a civil PE. Some states have roster desiginations where your stamp might reflect "Transportation Engineer" or "Geotechnical Engineer". But roster desigations are meaningless in effect. Because a Civil PE is a Civil PE and as far as I know, all of the roster desigination states don't actually treat the individual licenses any differently.
In fact most states don't recognize the difference between any PE discipline. IE, a PE having taken the Mechanical exam is not treated or licensed or effectively any different than a PE who took the Civil/Structural PE or anything else. Obviously there is that whole "ethics" thing where your not supposed to design things outside your area of expertise, in terms of actual licensing many states don't know or care, they just know your a professional and your expected to figure out what your a professional in.
So I would take whatever you think you're best at, whatever you think you'll do in the future.. basically whatever combination of Civil Exams you feel is best suited for you.