I used to use Hotels.com exclusively because I often found better deals. But as the noise has grown around horror stories from booking using third-party sites, I’ve sworn off them. Most of the time, it won’t be a problem — but when there is a problem, it can be almost impossible to find a solution.
Which is to say there’s a risk when booking using a third-party site — but you have to decide whether that risk is outweighed by the potential savings.