This, indeed, looks like a poor design solution. There may be a lot of reasons why they did this, but the mech. engineer should have been more creative. These exhaust mufflers, though, need to be in an horizontal position at the end. One thing is to avoid rainwater from coming into the system. We may not know the reason behind why they did this. Probably the location, distance of the equipment to the roof, penetration of fire-rated assemblies, etc.

But this too can be installed in the roof deck. They could have just "boxed-in" or enclosed the two pipes with some type of a non-combustible, properly flashed and waterproofed wall, with its top sloped, and terminated the pipes horizontally somewhere in the middle of the wall. But this seems to be a more expensive solution though.