It's frustrating when hotels don't have rooms ready by their posted check in time -- but it does happen. Normally it's the room that they have allocated for you (as an upgrade, etc) or in Marriott's case where bed type is guaranteed they only have two bed rooms available when you reserved a king size. Almost all those times I can either take a room that doesn't meet my preferences/upgrade to check in when I arrive (as long as it is after the posted check in time, normally 3 or 4pm).
However, it has happened to me where I've had to wait LONG after check in time because rooms were simply not ready. It's only happened once or twice and its always been a non-brand hotel where I don't have much way to complain.
tl;dr I don't think a check in time is guaranteed. But if delayed you can usually ask for a different type of room or the non-upgraded room.