They do seem to run ROTR a little later on EMH nights, but that's more in the vein of instead of calling the last BG 100 minutes before closing they call it 75 minutes before (regular) closing. They ran into EMH on at least 1 day that the ride experiences unusually high downtime and they still hadn't called all the "guaranteed" groups, but just until they got the last regular group called.
Just an FYI during evening EMH only hotel guests can enter rides, shows, and indoor character meets, but non-resort guests can still eat, shop, meet Woody, Buzz, and Jessie, and watch the Star Wars fireworks, and many people do.