I'm not entirely sure about where the imagery of "up/down" originated. I'm going to guess that it has something to do with ancient belief in "the Underworld"...the dead went to the Underworld, I'm thinking specifically Hades, which was not a very shiny happy place. But other "Realms of the Dead" were almost commonly thought to be underground.
If "Hell" was associated with going "down" to the underworld it makes sense that the opposite of Hell would be the opposite direction.
Similarly, most every religion of ancient civilizations of the known world, "fathers" or "kings" of gods were almost universally sky deities: Odin, Zeus/Jupiter, Ra. Hence, the Father, the Light, the "Good guys" were "up."
As to whether I've ever run a dungeon with levels that actually reached the Abyssal or Infernal planes...I have not run them, but they do exist.
Specifically, I have a region in my world (Thole "the Broken Lands") that is is entirely consumed in evil. It is rumored there are (and there actually are) "[super]naturally occurring" stable portals to various planes of the nether regions, the abyss, the elemental planes of Fire or Smoke, the "Grey Lands"/River of the Dead (where souls of the dead of Orea must travel before being judged by the goddess of Death at the fork in the river to go down one branch to the Higher Planes or the other to the Lower), the plane of Shadow and possibly other sinister/not so nice places.
Though I haven't detailed these sorts of portals existing in other places in the world, there is no reason there might not be...i.e. Travel far enough beneath the seas, you might find yourself inadvertently passing into the elemental plane of water. On a windy crag at the highest point of some mountain you might pass through a cloud bank to find yourselves in the elemental plane of air...
I like to keep as many possibilities open as...well, possible.
So planar travel without plane-traveling magic is definitely an option...though few are foolish enough to attempt it, particularly traveling into Thole (which only the very evil or very mad would dare to do).
--SD