They're not exactly deprecated, they just don't install automatically anymore. As I read it (and use them in npm 3), they're a way to specify "you need this other library installed also" without actually installing it.
In a lot of cases ("we just need some flavor of jQuery 2"), of which I am not sure that this us-web thing is an example, it's handy. The thing you're distributing isn't standalone, it's a thing people will use in an environment that has some installed jquery already, so you're fine.
The way I see it, if you're using a library that you can specify very permissively, peer dependencies are quite handy, and in this particular case seem useful - I'm building some webapp, I need to know that my UI library wants jquery to work, but I have a choice of not necessarily using that part (probably used for DOM manipulation, so if I'm just npm installing it for the CSS, wev), or making sure I meet the dependency with the other stuff I'm using. If not installed by default is a problem, there's an npm-install-peers package that does that.
In a lot of cases ("we just need some flavor of jQuery 2"), of which I am not sure that this us-web thing is an example, it's handy. The thing you're distributing isn't standalone, it's a thing people will use in an environment that has some installed jquery already, so you're fine.
The way I see it, if you're using a library that you can specify very permissively, peer dependencies are quite handy, and in this particular case seem useful - I'm building some webapp, I need to know that my UI library wants jquery to work, but I have a choice of not necessarily using that part (probably used for DOM manipulation, so if I'm just npm installing it for the CSS, wev), or making sure I meet the dependency with the other stuff I'm using. If not installed by default is a problem, there's an npm-install-peers package that does that.