Using the javascript: protocol affects accessibility, and also hurts how SEO friendly your page is.
Take note that HTML stands for Hypter Text something something... Hyper Text denotes text with links and references in it, which is what an anchor element <a> is used for.
When you use the javascript: 'protocol' you're misusing the anchor element. Since you're misusing the <a> element, things like the Google Bot and the Jaws Screen reader will have trouble 'understanding' your page, since they don't care much about your JS but care plenty about the Hyper Text ML, taking special note of the anchor hrefs.
It also affects the usability of your page when a user who does not have JavaScript enabled visits your page; you're breaking the expected functionality and behavior of links for those users. It will look like a link, but it won't act like a link because it uses the javascript protocol.
You might think "but how many people have JavaScript disabled nowadays?" but I like to phrase that idea more along the lines of "How many potential customers am I willing to turn away just because of a checkbox in their browser settings?"
It boils down to how href is an HTML attribute, and as such it belongs to your site's information, not its behavior. The JavaScript defines the behavior, but your never want it to interfere with the data/information. The epitome of this idea would be the external JavaScript file; not using onclick as an attribute, but instead as an event handler in your JavaScript file.