I've seen this theory offered up before. Since I don't breed, I can't offer any personal experience or anecdotes, but I do believe the theory has strong merit and I also would be interested in hearing from anyone with a large enough pool of experience with cut and uncut eggs to offer up their point of view.
While it IS a common practice to cut ball python eggs, I think it's wrong to say "everyone" does it. IF someone is cutting eggs, they are far more likely to post pictures of it. So you see lots of pictures of cut eggs. But anyone who doesn't cut eggs isn't going to give daily updates about the eggs they didn't cut. So it only LOOKS like "everyone" is doing it, because those that don't aren't bothering to talk about it except in threads like this.