Indeed, and this issue is about to expload when the canvas column type will soon be made available; it will have the opposite affect – the definition of a cell will contain the content of a full page. I suspect the Codans have already pondered this implication in great detail.
But in as much as the intra-hyperlinking capabilities are transformative, they may be overwhelming for new users attempting to decide how best to organize information. In that sense, there is probably a case for identifying some “best practices”, a term that is bit inappropriate because it is too constrained to serve in a valuable way given the information architectures that are possible with Coda.
In contrast, I tend to tilt toward the term “success patterns” - a collection of smart ways to embrace and organize information to meet specific business requirements. I think this is more about how your target users relate to the information in the context of getting stuff done. There is no right way perhaps, but there are certainly some bad ways.