These all seem like issues that are obvious in hindsight but may not have been obvious at the time. It's much easier to look at an existing, established codebase and point out all the flaws that it is to anticipate all the future challenges. In other words, you're monday-morning quarterbacking.

Maybe Notch didn't start building it with the idea that anyone would want to mod it. Heck, maybe he didn't even anticipate that it would be popular enough to require great performance. If he expected the game to be played primarily by him and a few friends then he could forego performance for beefier machines.

If he started out trying to build a game that would need to be extremely easy to mod and be performant on millions of machines of varying performance capabilities, he probably wouldn't have gotten around to actually writing it in the first place. It's called over-engineering, and it kills more projects than anything else, IMO.