Single Universe Theory

Ocarina of Time and probably Majora's Mask appear to lack parallel universes (unless you consider some of the shenanigans possible with Farore's Wind Wrong Warping as being a form of parallel universes). While I'm not 100% confident that parallel universes can't exist in some form, I'm pretty sure they don't exist for two reasons:

The first and most important reason is how collision is done on surfaces. While collision surface polygon data is still stored as short values, there is also a bounding box defined around each collision mesh collection, in the form of min and max x,y,z coordinates. If Link's coordinates are "outside" the bounding box (not sure what counts as outside, but it's only a few units), the collection is skipped over. On file these min/max coordinates are stored as short values as well, but when the collision mesh is loaded into memory, they are upcast to integer values. I believe during the collision check routine, they are further upcast to floating point values, but I'm not sure.

The second reason applies to "vertical" parallel universes. For collision checking purposes, Link's actor performs a straight down raycast to detect the surface immediately beneath him. As Link's Y axis increases, the computation time for the raycast increases, until Link reaches a point where the raycast routine is unable to decrement the Y coordinate check and enters an infinite loop.

One thing I'm not sure of is that I've heard that the game will crash at relatively low Y coordinates on N64 hardware (possible when riding the "rocket chest"), which would prevent the above from being even possible on N64.