Hundreds of hidden links in navigation bar (not spam links)

I have been recently tasked with taking over the design of our company website, but noticed it loads rather slowly. I checked the HTML source on the home page, and I see that the site is loading every single page as a hidden link (hundreds upon hundreds of them). I found the source of the link hiding in our CSS under
#menus ul ul {display: none}

If I set it to display: block, all of the links suddenly become visible in the nav bar on the site.

I know Google penalizes sites that do something like this as well, which is a huge issue.

Is there a place in the wordpress code that I can turn off these links from even being generated? I’m a quasi-newbie to backend coding of wordpress itself, so I wasn’t sure if this was a simple task or not.

If you’d like to see the problem first hand, my site is still in design at 4.71.46.151 (http).

Any help is greatly appreciated.