Same with lexical scoping? Not really following you.
(Or, in short, what you're doing each time you're setting environment variables in a shell call. Environment variables are dynamic scoping, just one level up.)
Namespaces are mostly fine if they're only helping against name clashes, and not trying to do access control. Even then, given the Lisp nature and high extensibility of Emacs (two sides of the same coin, actually), normal namespaces you see in other programming languages are a bad fit, as they don't play well with symbols and various patterns around using symbols as designators resolved at runtime. You'd need a namespacing solution like packages in Common Lisp, which is quite different than what people are used to.
In general, none of that would be a show-stopper - it's more that Emacs always leaned on being easy to extend, including extend interactively (via REPL, or more commonly, just selecting and eval-ing blocks of code), and things like namespaces tend to make it more annoying.