There are a few annoyances with getting an ad-free version of an article from Safari into DEVONthink: in Sierra, Safari always demands to know “are you sure” when you invoke the clipper. The “Instapaper” option doesn’t work many times, and when it does work all the articles have the ugly “Instapaper” header.
There’s a better way. First thing is to set up a keyboard shortcut in System preferences in Keyboard > Shortcuts > App Shortcuts > All Applications for the Print > PDF > Save PDF to DEVONthink Pro command. I use [size=150]⇧⌥⌘V[/size], but anything will do. Notice that this shortcut is only activated when you are in a macOS print dialog – so it will not interfere with other applications.
Once done, then you browse to a page you want to keep, press [size=150]⇧⌘R[/size] to enter Reader mode. Press [size=150]⌘P[/size] to open the Print dialog. Press [size=150]⇧⌥⌘V[/size] to send the PDF to DEVONthink. These three actions can be strung together with Keyboard Maestro, Typinator, Text Expander, or your other favorite macro tool.