Actually, "Boom Town" in Season 27 (New Series 1) referenced the New Series novel the Monsters Inside.
Are we missing the fact that the whole "Human nature" 2 part story in season 3 with John Smith and Martha was a re written version of a book that was written about the 7th Doctor? Leading in turn to the whole "Big reveal" of that season being possible? yes, the extended universe is referenced a fair bit in the new series of who.
That's twice, not what I'd call a "fair bit."
There are plenty smaller examples. For example, the Daleks never used "rels" on the classic TV show (although they did in the Peter Cushing movies), but they did in the spinoff novels and audios, and now they do on the revived series. The writers do lots of "throwaway" references like this to keep the hardcore fans happy without confusing the casual viewers.
"Human Nature": A rewrite isn't a reference in the sense of accepting events as part of the show's background. Had the Doctor spoken of the events of the book as having happened in his past, that would have been such a reference. A rewrite says, in effect: those events did not happen in the Doctor's past but the idea is so good we want to use it in his present.
The Series 5 story "The Lodger" is a similar case. I believe the original graphic story featured Mickey Smith.
The "throwaway" references ("rels", etc.) likewise endorse the value of particular ideas without importing into the show the events of the stories in which those ideas first appeared.