They use arrays for static vertex, texture, etc. data to send to the GPU. They don't use arrays for things that are being created and destroyed all the time, such as units in a strategy game, they use lists for those things.
But do they use linked lists for them? I would have assumed you would use an arena for something like that, precisely because you already need to iterate over all of them and can represent any graph as keys into a generational index, so that reading stale keys is trivially handled.
Again, I'm not a game dev and this is just my understanding after reading up on these topics after watching https://youtu.be/aKLntZcp27M.
They certainly used linked lists all over the place in StarCraft, WarCraft, and Diablo [1]. I don't know that many game developers would use complicated data structures like the one you've described here. Linked lists are fantastic for insertion/removal in arbitrary places.
Game development is not really about showing off with cutting-edge CS research, it's about getting things done. Maybe your arenas with generational indices would be better, but they could take a long time to figure out and lead to a big mess that doesn't go anywhere.
Arenas aren't "cutting edge CS research," theyre used widely in latency-sensitive applications like gaming.
This article [1] describes how to implement one for a game engine.
Basic versions are easy to understand and provide good results.
Starcraft/etc. are 20+ year old games and software development patterns as well as gaming hardware have changed in fundamental ways since then.
Conventional wisdom nowadays is that cache misses on every list iteration are a lot worse than shuffling a few contiguous bytes around or marking things inactive when removing items.
+ Game engines use complex data structures and algorithms. Some are cutting-edge research implemented from papers, specially in graphics.
+ A generational index is not complex.
Yes, game development (as opposed to game engine development or video/audio rendering) is a mess. That does not mean the actual technical fields involved are simple.