His diary is one of the most entertaining historical sources I've ever read so I'm not at all surprised that Stephenson found a way to work it in. (One part of the diary that I remember thinking felt like a novel was when he rushes to bury his prized Italian olive oil in his backyard during the Great Fire of London.)
The whole thing's online and cross-referenced here by the way, highly recommended:
http://www.pepysdiary.com/