I don't have experience w/ day care nor am I in Canada. But, dh & I were just talking tonight at dinner about how people expect others to care for their children like they would. I would not take for granted that the day care workers know what you want done w/ your son.
Have you looked through all of their information on diapering? If they haven't given anything to you (& they do not have anything listed on their website), then I would call (or go to talk) & ask to speak to whomever is in charge of the room your son will be in to ask what the diapering procedure is. Then you can decide what to say from there. A simple, "how do you handle an intact penis?" would probably get you on your way to finding out how they handle things.