I've used Agoda about 50 times, and have only had one conflict, which was actually similar to what you described with hotels.com.
Print or at least, take a screen shot of the confirmation email. If the hotel/hostel did end up being sold out for the night, Agoda will certainly help you (in my case, I got a refund within two business days). As a back-up plan, take down a few addresses of alternate places to stay, preferably in the local language too.