Node API yes, NPM library no. If you add a dependency on a library that uses NPM you now depend on an entire web of transitive NPM dependencies, with all of the problems that entails. People don't dislike NPM because it's aesthetically displeasing—you can't just abstract away the problems with NPM. The ecosystem causes real problems with real software, and Deno initially recognized those real problems and set out to reset the ecosystem.
The only way in which NPM-compat is different than colored functions is that there's no static compiler feature telling you when you've added a dependency on a bunch of NPM libraries.
Though, it is nicer if it’s on jsr.io because you’ll see Typescript source code in the debugger.
There’s nothing about starting over that prevents ending up with a whole new rat’s nest of dependencies, if you’re not careful.
So it reminds me more of trying to avoid CGO in Go or avoid “unsafe” in Rust.
It would be worse if Node-specific types started appearing as function parameters or return types, but that seems fairly rare even in npm libraries, so it seems easy to avoid.