How can I block email signup overlays or javascript popups in Safari?
...are there extensions that will simply block sites that utilize
  these modal popups?


The problem here is that they are not pop-ups as what you are traditionally used to.  They are basically HTML elements that are overlayed over the parent HTML document.

Block the modal popup

What makes this extremely difficult to block is that site functionality may depend on it.  Some modals may contain nonsense while others might have important information (i.e. shopping cart, contact form, etc.)

Chrome/Firefox has a plugin called Behind the Overlay but results are spotty at best.  I don't know of any for Safari.

Closing the tab

This really wouldn't be workable since this isn't a popup of a new window/tab - it's an HTML element in the same document.  Closing the tab would close out the whole session on that webpage.

Block site from search results

This is a function of the search engine and not of Safari.  Most HTML 5 compliant sites now use these modals so blocking the sites would be counter productive.  However, if there is a site you wish to ignore because of their use of modals, you can exclude it in your search query (Bing, Google, DuckDuckGo)

Macbook Pro -apple.com