I had read somewhere about why to use one over the other but what do most prefer and what's the reasoning on using one over the other?

A horizontal eye makes the lure stand up when you drag it, the vertical eye will let it fall on its side. Try it in some shallow water of a fishtank and you will see what I mean.

You'll aslo get more, and better hook-ups with the horizontal eye!!  Mostly because of the same reason that Thefishy1 said!  The shakey head with a horizontal hook eye almost always comes straight up, where the vertical hook will sometimes turn leading to missed fish or poor hook-ups!

With that said, I've caught many fish with both types of hooks, but definately prefer the horizontal hook eye!