Define "big project" and a way to measure how large it is.

Google Maps is big? I'm pretty sure it uses a lot of JavaScript.

A 3D modelling app? https://clara.io/

I don't think there's a limit for JS files. But you can easily work with more than one JS file if that becomes a problem. Also, "lines" don't exists when the browser parses a JS file, as I said before, if you look at the minified .js file of jQuery (and all minified files I guess) you'll see it has only 4 lines and the first one is a comment.

Maybe you have limits if you're making a web app and the JS file must be read from a server. The server might have a limit for the size of files it sends to the clients, but it will be a server limitation, not JavaScript.

Another thing I remember that I do think it's an advantage: Since you run it in a browser it's easy so access the HTML and CSS content of a page, so you can build your app with them too. You can add HTML buttons over the canvas with some CSS and use them as part of your app. You can use WebGL and the canvas to do the 3D part of a game and HTML and CSS to draw the GUI over it.