We've used Agoda quite a few times in the past, generally to book hotels in Asia, but not within the last decade so consider my comments with caution. (I pulled up our last booking which was for Seoul in 2015 and I still get their marketing spam weekly.) We generally try to book directly with the hotel nowadays but in the past, for us it seemed more difficult to find/book certain hotels, particularly smaller/boutique hotels in Asia. I'm assuming it was due to the difficulty in setting up/maintaining a website in English with booking, inventory, and payment systems integrated back in the day.
We've also used Booking.com and initially commented how similiar they were (other than one including the taxes in the initial price quotes). So it wasn't a surprise when we found out they were part of the same travel conglomerate.
We haven't cancelled a booking with Agoda but vaguely recall a friend did without issues. And I don't recall any general issues with any of our bookings.
While I would consider booking on Agoda again, I think it's fairly understood nowadays that hotels will generally match prices you find on third party booking sites. But you never know what's happening in the background: Eg. The hotel has an arrangement to hold some rooms for the third party booking site, the third party booking site gets a discounted rate to pass on to their customer because of the volume they drive to the hotel, etc.
