To truly achieve the same thing as "tree shaking," the function call overhead would be abysmal. You'd have to check whether the module was loaded already (with synchronization if your program is multithreaded). For single threaded programs, you could avoid this by hot-patching your machine code, but there's no way around some synchronization barrier in multithreaded programs [1]. In JavaScript (or any language where you want to avoid sending a large bundle over the network), you'd incur the latency of a network request for the first call to any function.

You're right that people are already splitting apps into bundles, but that is usually done at the page level.

[1] You could probably avoid having to take a mutex after the first call to the function with self patching code, but that sounds incredibly ugly and could have other implications (self-modifying code could be detected as a virus; could be used as a gadget to exploit some other vulnerability).