But even if it does only affect a small number of guests (lets be conservative and say a few thousand), that small number of guests are the ones who shelled out BIG BUCKS to stay at a monorail resort, of which EMH is a heavily marketed perk of staying there as well as monorail access.
So the number of guests it affects is largely irrelevant because they paid for access.
I believe if you review printed material, staying on property gives you access to use Disney Transportation. I do not believe, but I may be wrong, that there are any guarantees what transportation it is or when it is available.