Web clips sometimes do not have blank margins, this makes them look ugly in DEVONthink.
Ask for help: how to make webarchives displayed in DEVONthink always with default margins?
Web archives just use the layout of the original web page. One possibility might be to use a custom CSS (see Preferences > Web) specifying the desired margins. Depending on the web page you could also try to capture a clutter-free version.