Since Writing Is A Way To Record Thought Through Language, and the whole point of Linked Notes is to use Writing as a user interface that facilitates thinking, related notes should be connected together.

Similar to how a train of thoughts take you from A to B to Y to C, conceptually related notes should be linked together. Being able to follow associative trails of thought and information increases ideation and creation.

When we Keep all notes in a single folder with no hierarchical structure, links define relationships between Linked Notes, and the quality of the links defines the utility of the entire system.

As Niklas Luhmann said:

Each note is just an element that derives its quality from the network of links in the system. A note that is not connected to the network will be lost, will be forgotten by the Zettelkasten.

The practice of linking itself helps memorizing your notes: Maintaining linked notes loosely resembles spaced repetition.

Adding a new note whenever it feels necessary can be high-friction, reducing the likelihood of doing it. You can use empty notes, since Backlinks can create implicit nodes in networked notes.

Also, when Note titles should be a tiny summary of their content, you can easily integrate linking into the relevant passage of each note as I am doing right now, as opposed to e.g. linking relevant notes at the end of the current one. Integrating linking in the passage makes it very easy to keep the principle that Notes should be atomic, since at any point you realize a note is too diffused and you need to break it down, the links will take care of themselves. If the links are at the end of each note, you need to manually carry over the relevant ones to the extracted note.