What I usually do is add the part externally. Resistors are small and cheap, and I'll often want that behavior to be effective during resets or code crash. For an input (where state during boot-up doesn't matter), I might leave it off the schematic, but I personally like the suggestion of adding the part anyway, then maybe noting it with an asterisk and a footnote that says "optional if internal pull-ups are enabled".
That said, I would be happy reading a schematic where any of the above methods were used.