This is a valid concern for some of the smaller places and your best bet would be to email or call the hotel to confirm.

I've had 3 "surprises" out of 50+ Agoda bookings - all 3 of which involved very small mom-and-pop hotels and last-minute booking (usually early morning of the day of arrival with the arrival being in the evening) - it was usually a question of the hotel not keeping the inventory up-to-date in Agoda's system .

In all 3 cases either the hotel or Agoda were able to resolve the problem promptly and with very minimal inconvenience .