Shuffling zk (Zettelkasten) cards is just fine. [1] The meaning of a note is largely determined by its connections, and so approaching a note through a different set of connections gives it a different meaning. Finding new paths uncovers new meanings, which is at least one of the zk points. Shuffling cards is one way you might find new paths.

[1] If you have physical cards you are destroying the default hierarchical path if you shuffle them and that could be a pain in arse to reconstruct, and your ability to find a note with physical cards also depends on the hierarchy. Digital cards have different problems.