Next time you use a mapping app and scroll with your fingers or thumb, pay close attention to the direction: Most likely you're actually dragging it slightly diagonally then adjusting vertically afterwards.
I think a large part of it is that horizontal navigation as in OP is too thin, so if you do these natural dragging shapes your finger leaves the scrollable area. It may still work fine, but it feels wrong. Vertical scrolling on the other hand, because of what you say with our writing style, has a much larger grab area so we can easily stay within the box.
There's also parts specific to it being a menu: A vertically-aligned one usually has empty space on the right because the menu items probably aren't the same length, giving you a nice "grab area" (either your finger with touch or a place to put the mouse pointer for a scrollwheel) that doesn't hide anything. Plus scanning down a list is easier than sideways anyway because every item starts at the same place; just imagine how annoying it is to read a bulleted list on here when someone accidentally puts it all on one line because they didn't add an extra blank line between bullets.