This answer is primarily about the WebPageElement types (like SiteNavigationElement).
For WebPage, see my answer to the question Implicity of web page structure in Schema.org (tl;dr: it can be useful to provide WebPage, even for the current page).
For WebSite, similar reasons from the answer above apply. HTML doesn’t allow you to state something about the whole site (and, by the way, a Google rich result makes use of this type).
Schema.org is not restricted to HTML5.
Schema.org is a vocabulary which can be used with various syntaxes (like JSON-LD, Microdata, RDFa, Turtle, …), stand-alone or in various host languages (like HTML 4.01, XHTML 1.0/1.1, (X)HTML5, XML, SVG, …). So having other ways to specify that something is (or: is about; or: represents) a site-wide navigation, a table etc. is the exception rather than the rule.
But there can be reasons to use these types even in HTML5 documents, for example:
The HTML5 markup and the annotations from Microdata/RDFa are two "different worlds": a Microdata/RDFa parser is only interested in the annotations, and after successfully parsing a document, the underlying markup is of no relevance anymore (e.g., the information that something was specified in a table element is lost in the Microdata/RDFa layer).
By using types like WebPageElement, you can specify metadata that is not possible to specify in plain HTML5. For example, the author/license/etc. of a table.
You can use these types to specify data about something which does not exist on the current document, e.g., you could say on your personal website that you are the author of a table in Wikipedia.
That said, these are not typical use cases relevant for a broad range of authors. Unless you have a specific reason for using them, you might want to omit them. They are not useful for typical websites. Using them can even be problematic in some cases.
See also my Schema.org issue The purpose of WebPageElement and mainContentOfPage, where I suggested to deprecate WebPageElement and the mainContentOfPage property.
与恶龙缠斗过久,自身亦成为恶龙；凝视深渊过久,深渊将回以凝视…
