Scripts + NPM are better together, for example because scripts executed under NPM have the local packages binaries in the path. This makes it very easy to have a fully locally installed build environment with no system dependencies. And if you do use webpack, it also helps in providing a uniform interface (Is "test" a Webpack target or a script? Who cares, just use "npm test", it'll work either way, also if we change it in the future).

And it's not an either-or case in the real world. Our company has a big Webpack config that does a lot, and still we have 15+ scripts as well (static analysis, inserting copyright headers, sourcemap uploads, 3rd party vendoring, release scripts...). Some things are better in WP (building), while some things are just simpler with a shell script.