This is purely my hypotheses, so take it for what it's worth. I think that it has to do with people who either A) don't know about EMH or B) are limited by schedules and need to go to that park on that day, but aren't able to get up that early. Let's just say that on any given day 10,000 people go to MK. Now, on EE day, let's say 5,000 resort guests decide that they're going to go to MK for EE. So from 8-9 there are 5,000 people in the park. Then, at 9 am, the other 10,000 start showing up. By they time they're all in, you now have 15,000, when on a non-EE day you'd only have 10,000, so it's more crowded.
Another thought about the afternoon, if I know about EE, won't make it up in time for that, but need to hit that park that day for whatever reason, I probably would come to the park afternoon, hoping that by that time many of the EE patrons would have left for their afternoon break.
I have never done EE and always avoid the EE park at all costs. But sometimes it's your only day to do a certain ride, so you bite the bullet. And like I said, there are lots of non-resort guest and non-planners who know nothing about EE and they just go where they feel like it.