The thing to understand is that generally the site title has h1 and the title of a content instance has h2, so really within the content we usually only want to use h3, h4, h5. As discussed in the article Customizing the Editor Toolbars we actually are mapping the h1 - h3 as h3-h5 since most end users don't know much about html, though you can override this if you really wanted to.
I should note also though that though that article shows web.config/user.config settings for those mappings, in the latest source code we stopped using those settings and just do the mapping from ckeditor-mojoconfig.js so it will work a little different in the next release and overriding it will mean overriding the path to that js file so it points to your own custom version of it.
Style templates are a different thing, if you create a style template for the element h3, that style element will only be available in the style dropdown when you have selected an h3 element in the editor. It is useful for adding a css class to the selected element.
Hope that helps,