In my experience they're pretty rare. Not many Node packages need a native build (mostly node-sass in my experience, which has now been deprecated in favor of a Dart implementation which I believe compiles to JavaScript), and I don't think Deno even supports importing non-JS/WASM modules to begin with, so that type of problem should be fully impossible here
I think there's still a meaningful difference between runtime plugins (which to my understanding have to exist locally on the file system, outside of normal dependencies) vs normal dependencies that just sometimes have a native component. Deno projects won't occasionally accidentally have a native dependency like Node projects do; adding one will be a Big Deal that you choose to do on purpose, probably reserved for extreme cases, and for those special cases maybe you also choose to bail out and use Docker
