It has always been this way, largely depending on the pathing around the node. Typically, I will run just past the node and then back up my main so that the pets are all on the far side of the node. If your camera view is set up properly, your view is far enough back that you can see to click.
On steep slopes, it's difficult not only for pet issues but getting your cameras lined up properly even between followers if you aren't perfectly stacked up.
TL;DR = there's no easy answer, and there is no way to make your pet "click-through" like you can with a chat window. And don't get me started on tree limbs and other objects in the way when questing in places like Suramar or Talador buildings.
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