Knots play an important role in fundamental physics. Here are a few examples: link1, link2, link3, link4, link5. Hence, it should be expected that knots will appear in someplace in the Wolfram Model, where they will be physically relevant. Maybe these knots are "encrypted" as properties of the spatial hypergraph, causal graph and multiway system. Any proposal of how to find these knots is welcome.
If you are interested in another definition of fundamental particles as braiding of space, I suggest looking into Sundance Bilson-Thompson's work. Just a few of his works are listed below.
Emergent Braided Matter of Quantum Geometry
Particle Topology, Braids and Braided Belts
Particle Identifications from Symmetries of Braided Ribbon Network Invariants