In the vast majority of cases, the watermark data wouldn't point anywhere interesting. Maybe the serial number would point to a public library or a warehouse where the printer was stored prior to sale. Certainly The Intercept had no way of knowing that the serial number would correspond to an office printer at the NSA or one of their contractors.

I don't think we should expect news outlets to scour every printed document for these watermarks and remove them. Most aren't that technically savvy and this solidly seems like the responsibility of the person doing the leaking.

Leaking is dangerous and risky. I don't know the leaker personally but I could understand someone feeling that documents need to be released to the public and, at the same time, feeling like they can't evade the NSA's investigation. At that point any counter-measures probably seem pointless, especially for those who are not technical and can't imagine any bounds to the NSA investigative powers.