We didn't really noticed when on vacation in Canada before, but now were struck: how do people here manage those long drives if there are no parking lots with (or even without) washrooms to have a pause?

I understand that most of non-400 highways feature wide shoulders to stop and after all no one will be surprised to see a vehicle stopped right on a ramp to let the kids do numbers one and so on, but anyways? Driving on QEW to Niagara, we've seen only a couple of gas stations and fast food outlets perhaps 1 km away from some exit, but that was all. Maybe it's better on 407?

Highways are a provincial jurisdiction, so it really varies upon the province. I know that in Quebec, there are rest stops with washrooms. In BC there are some rest stops with washrooms, but most provincial parks have washroom facilities, so we often take advantage of those as we often pass by various provincial parks when travelling long distances. Otherwise, gas stations or fast food restaurants do the trick.

Definitely an annoyance on the stretch of QEW between Buffalo and Toronto. McDonalds/Harvey's/PetroCan are your best bets. The US Interstates are much better in this regard (dons asbestos pants).
When facing long drives, I adopt what I refer to as my Restroom Avoidance Protocol. No coffee in the morning, and minimal liquids en route. For some reason, Mrs. Bill thinks I'm weird...