This is the reason I hope booking.com are successful (they increasingly have aparthotel listings). They usually offer free cancellation and I've never had a problem cancelling for free if I had a good reason (such as illness).
Other thing to watch out for is fees. The place I'm staying at charges 20000yen ($150) if you enter the apartment without taking off your shoes, 6000yen ($44) per hour overstayed after checkout, and inviting anyone into the house for any amount of time causes your entire booking to triple in price ($2000 in my case). I'm not sure if they can enforce those...
They definitely cannot enforce those. Now if you do enter with shoes AND damage the floor a bit*, I still doubt they could even enforce those. Even courts here are not punitive in nature (they are restorative), so even if they sued you and won for going in with shoes, which I highly doubt, at most you'd have to pay for the damage they can prove that you made, which would be few thousand yens.
The only one I am a bit unsure is about guests, since they might technically be able to limit who goes around.
*if you do go with dirty shoes and make a mess is a different matter, I'm just talking about normal walking with shoes
I'm sure they had problems with people spreading dirt on the floor and a cleaning fee is perfectly reasonable, I just found the size of the penalties to be amusing.
Other thing to watch out for is fees. The place I'm staying at charges 20000yen ($150) if you enter the apartment without taking off your shoes, 6000yen ($44) per hour overstayed after checkout, and inviting anyone into the house for any amount of time causes your entire booking to triple in price ($2000 in my case). I'm not sure if they can enforce those...