I would say that counters apply to words, or more accurately, the concepts that those words represent, whether in the literal or abstract sense. The words ticket and きっぷ both represent a flat object which would use the 枚 counter. A digital representation of or a substitute for two tickets is still considered two tickets, especially if you yourself actually use the word 'ticket'.
I really don't see this as a Japanese-language specific question, as in English the same question could be asked. For an example, if you show up to a theater with a digital receipt and say 'I have two tickets to the show' is anybody going to misunderstand that you meant it in the abstract sense? Further, if I sent you an image of two pencils and asked you how many pencils there were, I would be justified to think you a bit too literal if you answered 'There are no pencils, only one image'.
About your email example, you received one email (一通）for the digital equivalent of two tickets （きっぷ2枚）. If you want to present it differently (more literally), you can say 2名分の入場券(1通).