The agency is still a third party and if something goes wrong with either the flight or the hotel, you are still having to deal with both. What happens if the hotel isn’t satisfactory?
Have not travelled for a while now, but the relatively tiny travel agency I used to use had a 24/7 support phone line. Did not personally have a need to use it, but a friend did, and the agency indeed handled the situation to his satisfaction.
Moreover, booking international flights through that agency somehow always ended up cheaper than what I could find myself, even when accounting for their fees.
The agency isn’t going to do anything for you.