I guess a good alternative is to have the build tools refuse to do anything until the user/developer has installed the proper hooks by running ./init-hooks (as opposed to executing ./init-hooks silently in the background). I agree that's a preferable way to do it in a public project: explicit is better than implicit
I agree, that sounds like a much better approach. In a private or companies internal project it's probably not an issue, you already "trust" the code you're downloading.
I tend to have some sort of setup or bootstrap script which the docs promote as the way to prepare for development. This tends to install any dev dependencies and also sets up hooks (which is always optional). This works fairly well in most cases, combine that with a lint on the CI and most people don't have any problems. It also saves assuming someone wants git hooks just because they're pulling code, often they just want to build and run it.
