I have Assassin's Creed Black Flag installed on my PC, and I'm looking to purchase Rogue. Because they look like they are built on the same engine, I am wondering if they share files to minimise disc space usage, like the Valve Source games do.
Separate games, regardless of how similar they might be or if they even have the exact same files, will never share those files. They will always be installed fully into their own folder and only read the files from there to run.
Even if the engine looks to be the same on 2 games there could be small differences in each's coding that makes a large difference and trying to swap out one game's code for another sounds like a quick way to cause immediate crashing on starting the game. It's probably best to leave the game files be unless you're getting into modding and know what you're doing.
The games are independent, you can install one without the other. It doesn't use less disc space.