One way is to maintain 2 sets of files: a normalized one with no redundancies and just references, and another one with everything fully rendered and expanded.

One way is to maintain 2 sets of files: a normalized one with no redundancies and just references, and another one with everything fully rendered and expanded. That second set is what you serve (bonus: it will be fully static); the first set is what you edit/maintain/search. This is essentially a handmade caching system for your content. Once you approach the problem that way, you can also consider other forms of caching, like having a dynamic, server-side generated site and a cache store sitting in front of it. That cache store can be some fancy caching system or it can be the output of a crawler than runs once a day against your dynamic site and outputs to a set of static html files that get served by your webserver.