If your site uses a few custom post types and those custom post types are viewable in the WordPress menu area, your admin panel can get messy quickly; making it hard to find categories or tags you actually want to include in your menus.
Of course you could alter your custom post type code to remove them from the menu item screen, but the easier solution is to use the SCREEN OPTIONS tab inside the menu admin area.
In the image above, you’ll see a screen options panel for a site that uses a WordPress ecommerce solution, an events calendar plugin, and Q&A forums. Each one of those plugins uses a custom post type that can be added to menus. Chances are your plugins which rely on custom post types include similar functionality.
The screen options drop down allows me to uncheck items I do not want on my menu admin screen, which I will do for events and products, two items I do not need to include in my main menu.
That makes my menu admin screen restrict available choices to just categories, tags, pages, and a few more standard options; and makes it easier to find what I need when I want to build out new menus.