I think it is self-evident that piracy has some effect on box office - people are very aware that you can watch a decent version online of a movie almost as soon as it's in cinemas, and naturally there are going to be some people who prefer to do that, compared to, say, 30 years ago where it was much more difficult to watch a movie outside of a cinema. Given how huge piracy is, it's impossible that it has no effect.
However, I don't believe that piracy has much effect on a case by case basis, it's more of a general issue. For a movie like Civil War, most people are gonna watch it on the big screen regardless of how soon the torrent is up, or what quality it is. But it's very difficult to establish just how great an effect piracy does or doesn't have.
As for repeat viewing effects? Like said above, the number of people who re-watch a movie several times in its first theatrical run is marginal at best. And though I'm sure there are plenty of people who have rewatched Civil War online already, you have to ask yourself if those people would really have gone to see it again if the stream wasn't available. An illegal viewing doesn't equate to a lost sale.
Moreover, it is essentially impossible to track which box office sales are rewatches - they are just sold as normal tickets. There are so many factors as to why a movie might have shortened legs that you can't just pin it on piracy. Hell, Batman v Superman, a near-identical movie to Civil War, had no HD stream upon release and Civil War is legging it out far better than that movie.