I generally agree with the sentiment that the line shown when choosing a target is silly and doesn't properly reflect the trajectory that the projectile should have. However, I do not feel like this is an issue, because I do not expect the "targetting line" to show me a fully accurate trajectory of the arrow. It's just a targetting line.

It also usually works in your favor: when the arrow arcs this way when you shoot, you can still shoot an enemy who is behind some small obstacles.