As with all things Disney, it depends on where you are. If you are near a major show when it lets out, chances are there might be a line. If you're tucked away in some selcuded cove, you are not likely to see a line no matter what's going on around you.
I've been at the busiest times and still not had to deal with lines in the bathrooms. It's happened a few times but isn't something I'd worry about too much. There are plenty of bathrooms, plenty of stalls(even in the Ladies), and you're not likely to have a problem.