If she plans something to say, she won't be struck dumb next time, she'll speak out. If he's not stopped he will keep on doing it.
Perhaps the next time she hears unexpected noises upstairs when they are visiting, she could act she is afraid, and say so, out loud "There must be an intruder upstairs! You go and check!" As the oldest there, she is not going to confront a burglar herself, of course! When SiL is revealed, she could say that there is no-one in the downstairs loo, it is empty so he doesn't need to go upstairs - and add with a laugh that the rooms don't need tidying up there either or she won't be able to find anything.
If he doesn't take the hint she may have to repeat the process, and possibly say that she is grateful for him wanting to help tidying but she'd really rather do it herself.