You're right; most of the languages and platforms used for developing applications don't have reliable support for tree-shaking or fine-grained static linking. But there's hope for some of them.

When building Android applications, it's common to process the JVM bytecode with ProGuard before converting it to Dex bytecode. ProGuard includes a tree-shaking step. Sometimes it's necessary to tell ProGuard about specific classes or class members that it should leave alone, if they're accessed dynamically (e.g. using java.lang.reflect or Class.forName). But it's still better than nothing.

Likewise, .NET applications for the Windows Store are compiled to native code using .NET Native, and that compilation includes a tree-shaking step. This introduces some limitations on the use of reflection. I'm guessing similar limitations will apply to the native compilation option of .NET Core.

As for JavaScript, Google's Closure Compiler can do tree-shaking. But I don't know if the Closure Compiler's advanced mode works with any of the popular JavaScript libraries or frameworks, or just Google's Closure Library.