Just to clarify, the Kids Midway at the Ex does not open until 11 a.m. on weekdays. It used to also be 11 a.m. on weekends, but it appears they may have moved it up till 10 a.m.
Good bets with really young children at the Ex are mostly around the Kids Midway area. You can play drums and percussion instruments for free at one part of the long building; you can sign up to make pizza (and get a free slice of real pizza); they have various acts on the stage aimed at young children with lots of participation; there is usually a "circus" where the kids from the audience all get to pretend with simple props to be the circus lions or acrobats; there is usually a parade where the kids (but really their parents) carry large puppets around; there is a real normal playground with slides; there is a petting zoo where the kibble to feed the animals is expensive but visiting the animals is free.
The washrooms, unfortunately, are only located in the kids midway itself in a set of trailers. They have been kept well cleaned the last few years by an onsite attendant. It's important to know where they are, though, as it's not too close to the other activities.
The farm building is also good with very young children. I haven't been yet this year, but in the past they have had some really cool tricycles to peddle that make it seem like you are driving a horse drawn carriage (hard to explain but way cool). There also were some other activities especially meant for 5 and under. In addition there are sheep being sheared; cows being milked; various farm animals to see, etc. All of these activities are free with admission.
I'd be more concerned with crowds at the ferry dock for Toronto Island and with getting parking in the main lot at the zoo (overflow parking is a zillion miles away from the entrance: try to get there early!) than with crowds at the Ex. Your guys are a bit young (short in height) for many of the rides even at the Kids Midway, so I don't think the lines will be that much of an issue.
If it's going to be really hot at the zoo, they do have a splash park. The water is very cold but sometimes very welcome. Food choices are very limited at the zoo and the lines can be crazy long. I'd bring a picnic and just buy a treat.
Hope you have a great weekend!