It's certainly possible to create an application that's just a Cocoa window with a web view inside it, sure. Whether that can meaningfully be called a "Cocoa app" is debatable. Obviously things like the app menu would require some Cocoa glue code, so yes, there are limits to how much you could do in just HTML and JS.
You'd also have to think carefully about how you would handle localization (duplicating the entire HTML and JS source for each language isn't going to be desirable), and there are lots of interface constructs that would be much harder to create than they would be using Cocoa, and/or wouldn't feel native to someone used to the OS X look and feel. And you'll be giving up some performance by using an interpreted language, which may or may not matter for your application.
There are applications for OS X that are built that way, and they generally feel like bad ports; if your goal is to make something that feels like a real Mac application, it's probably not a good way to go.