I think the isolation and memory safety guarantees that worker threads (or Web Workers) provide are very welcome. The friction mainly comes from ergonomics, as pointed out in the article. So there’s definitely room for improvement there (even within the current constraints).
A worker thread or Web Worker runs in its own isolate, so it needs to initialise it by parsing and executing its entry point. I'm not quite sure whether that's something that already happens but you could imagine optimising this by caching or snapshotting the initial state of an isolate when multiple workers use the same entry point, so new workers can start faster.
That cannot be done with the original main thread isolate because usually the worker environment has both different capabilities than the main isolate and a different entry point.
If I have to handle 1000 files in a small CLI I would probably just use Node.js asynchronous IO in a single thread and let it handle platform specifics for me! You’ll get very good throughput without having to handle threads yourself.