As far as Bullet penetration goes, it could simply be a way for programmers to simplify the development process, and put less focus on what material should go where in order to in turn make level design also more simple? I remember back in HL2 was first shown in 2003, and they pride themselves by saying the world was built out of materials; meaning steel drums, and wood would interact with water like they would in real life. I think it's less about if we have the tech, and more "How does this affect the game in general?" Like you said though, earlier COD games did this, so why was it eliminated in later games? Your guess is as good as mine, but I'm going to say it was purely a technical reason in order to strive for better fidelity, at the expense of finer attention to detail in non-graphical areas.
I think physics systems on some level have stagnated in recent years due to the complexity of fidelity in games. Gamers want more fidelity, and that will come at the expense of physics. For example, GTAIV had some pretty nifty physics that were not used in GTAV (there's a comparison video about it on YT). Same is true for Just Cause 3 vs. Just Cause 4. I essence, they simplified some of the physics in both games, possibly to reduce complexity, and/or increase fidelity as the physics were already putting a strain on the rather limited CPU power as it was.
I don't recall if this was eventually patched or not, but I remember a similar comparison video where someone took Horizon: Zero Dawn, and compared the physics systems between it, and BotW. BotW had a much more in-depth, and sophisticated physics system the world was built around, whereas HZD was more about the fidelity at the expense of physics. While I am unsure if this is truly the case, I think physics, and graphics trade blows depending on the hardware used, and what I see is physics take more of a backseat (AI scripts, and some simple objects though still have their systems in place). But hey, this is also a world where Infinity Ward felt that Fish A.I. was something fancy, and had to be included when Super Mario 64 did this almost two decades ago. In fairness, Mario 64 likely was a simple script that said, "once Mario is within this distance of the Fish, the Fish begin moving away from player," and less that the fish had their own individual AI systems.
But anyway, I'm getting off topic here. Map Design I think is a lot more complicated, and I'm not sure what I can really say about it except that the size of the map I don't really care about. I think there are advantages to all sorts of approaches. For example, I'm going to say straight away that I am not a fan of the map design of Rogue Company, but you get what you pay for, or don't pay for I guess. RC is only a fill-in for if COD ever comes to Switch. As far as your point about COD: Ghost's large map, are you talking about the Island looking one with the castle in it? It was big enough so there wasn't always something going on, but it also made it nice to keep your distance, and the castle provided some decent times where mayhem could occur.
I guess I haven't really done a deep-dive into the methodology of level design, and what really works, or doesn't work.