> Java libraries which are binary blobs

Java libraries are JAR -> Java Archives. You can unzip them and there is JVM bytecode inside which can be decompiled. Not really binary blobs.

It probably is fair to say that the state-of-the-art tools for JS development today are at least 1-2 decades behind the state-of-the-art for programming more generally. Trying to build larger applications in JS is a relatively new thing, and a community full of people who are enthusiastic and keen to do new things but often lacking in experience with larger and more long-lived software systems is getting a crash course in what does and doesn't work at that scale. Give it another 5-10 years and/or the more dramatic replacement of JS with better languages if new possibilities like WebAssembly change the landscape, and hopefully more of the experience will transfer over and the tools will catch up.