WebArchive is a proprietary Apple file format that captures the HTML code and the images of a Web page, so that it can be displayed - including images - even offline.
HTML is the source code of a Web page. An HTML file cannot display images unless the computer is online so that they can be downloaded.
A bookmark is the URL of a Web page and contains no text. When invoked when the computer is online the bookmark will open the Web page in a browser.
One can also capture a Web page as PDF, or clip a selected area as plain text or rich text (my preferred mode).
If you have checked DEVONagent’s Preferences to import your Safari bookmarks the bookmarklets you installed in Safari are also available in DEVONagent in the Bookmarks slideout. But I generally prefer using the menu and contextual menu options already available in DEVONthink.