The PD code $[(2, 3, 1, 4), (4, 1, 3, 2)]$ seems to map to a non-unique knot diagram. I can describe the following two Hopf links
with different orientations with this same PD code. As I understand it, while a link diagram does not have a unique PD code, a given PD code should map to just one knot diagram. Am I missing something?

Yes, Hopf links have an orientation ambiguity when using the increasing-index orientation convention for unoriented PD codes. A sure way to avoid this ambiguity is to switch to oriented PD codes, where you could write
to unambiguously mean the first diagram in your linked image. There are details in the KnotTheory package's documentation: http://katlas.org/wiki/Planar_Diagrams
Another option is to have degree-2 nodes to disambiguate the orientation. For example,
Now there are at least three indices in each component.
This ambiguity also arises when a link is an obvious connect sum with a Hopf link. It's a known problem that Scott Morrison, one of the authors of KnotTheory, once warned me about.
For illustration, here are the four ways of interpreting orientations for the PD code
[(2,3,1,4), (4,1,3,2)]: