Where do you suspect the problem might be? I know that the memory latency is the primary issue for that engine. It sucked on the CPU of that era, it sucks on the steam deck, but it does not suck for most modern CPU because they have way more L3 cache and better latency outside of it (as the article states)
Fallout 3 has massive issues on any new operating system. There are unofficial patches and mods to fix that but Valve does not auto-install anything unofficial, even if it would make things far better.
I recently played through Death Stranding which is more recent, better graphics and seemingly better optimized than Fallout 3. I'm pretty sure if the CPU can handle Death Stranding (and other more complex games) without problem, it could handle Fallout 3 if the programming was on point.
It's important to not forget that Skyrim has been ported to an insane amount of consoles over the years, which includes engine and optimization updates. It's a very actively maintained game that from what I can tell mostly follows sensible design practices with current hardware.
Fallout 3(& by extension New Vegas) hasn't had that luxury; those games only got two releases (initial & "ultimate edition"), both of which running on an engine where the glue holding things together is duct tape and technical debt going back to Oblivion and it was released for a set of consoles that needed optimization to the degree where it was just easier to dump the entire world state as it changed into a save file instead of just storing the bare minimum[0]. That's the sort of optimization that will lead to bugs down the line as undocumented features and behaviors change (not to mention the already buggy release state of both games.)
[0]: Which in turn caused another infamous bug to pop up where the PS3 would run out of storage to keep individual game saves (the cap was something like 10mb) after playing for long enough.
Fallout 3 and New Vegas both have massive issues. You may be better off using Lutris with the GOG version on the Steam Deck and finding a config that installs the performance fix mods.
I tried performance patches for both FO3/FNV and couldn’t fix it for either. I believe it’s because every prefab that Bethesda renders requires a memory access on every frame. So areas with a ton of prefabs like Mr. House’s penthouse or rivet city market are extremely slow.
It checks out given the articles coverage of just how poor the memory latency is once you exceed the tiny 4MB cache.
There are ways to “fix” it but they tend to suck. You can crank the draw distance of objects to the minimum but if it’s not done dynamically then every other scene becomes terribly ugly/broken. You can also install mods that remove some of the clutter but how do you know which clutter to remove? Some of it is aesthetically important and the tone of the scene can change dramatically by randomly removing stuff.