Maybe don’t make a particular naming scheme mandatory but just use folder structure to organize namespaces:
Food (folder)
Pizza.md
Fruit (subfolder)
Apple.md
Banana.md
Same folder reference:
We are in Banana.md,
let's reference Apple:
[[Apple]]
Child folder reference:
We are in Pizza.md,
let's reference Apple:
[[Fruit/Apple]]
Parent folder reference:
We are in Apple.md,
let's reference Pizza.md:
[[../Pizza]]