On a radius rod I am not sure that it matters, as long as the clevis is angled to align with the rod.
Mounting it so the bolt is vertical is the safe way to do it. In this orientation the bolt should be inserted from the top so the head of the bolt is on top and the nut is on the bottom. If the nut were to loosen and fall off, gravity is still holding the bolt in place, hopefully long enough for you to do an inspection and notice the lack of a nut.
Mounting the bolt horizontally, if the nut were to loosen and fall off, vibration and movement could result in losing the bolt as well.
Seeing how inboard A-arm mounts were brought up, the correct way is with the bolt vertical. The forces of braking and acceleration on an A-arm create tension and compression in the tubes of the arms. With the bolt vertical and the body of the rod-end horizontal, all the forces go straight through the shank of the rod-end, to the ball, and into the bolt. This is radial loading, the strong direction for rod-ends.
If the bolt is horizontal and the body of the rod-end is vertical, the forces go through the shank of the rod-end, to the ball, but now the ball is trying to slide down the bolt. The ball will be restrained by the clevis, but we now have a force acting axially along the bolt, the weak direction for a rod end. If overloaded, the ball will pop out of the body. Suspension is often designed like this because it allows more suspension travel, but that does not make it right.