Unless of course the same number of people moving from screen 1 to screen 2 also moved in the opposite direction - in which case the numbers would be exactly the same.
I doubt whether the punters who do disappear into the toilets between movies then go into a different screen when they return actually give a monkey's about the potential fire risk.
And as far as the cinemas go, they are more likely to say that you aren't allowed to do it because they want you to pay to see a second film, rather than because if there is a fire the number of people in the particular screen doesn't add up to the number of tickets sold. After all, if this mythical fire breaks out and three people who should be watching the film are in the toilet, two are buying more sweets and four have buggered off home cos the film is crap then the numbers aren't going to add up anyway, are they?