After reading through this thread I was concerned about all my pencil written notes throughout my references. On a non-study night while I was watching TV, I started going through trying to highlight all the pencil markings. I probably spent 2 hours and got through half of one book. I decided it was a waste of time given that it is not an explicit NCEES or CA rule.
In the test (San Mateo, CA), the proctors checked all the calculators (I saw someone turn in their TI-83 to amnesty!) and some flipped through references to check for loose paper, but said nothing about markings, that I saw.
All of that said, if I was starting to study for the exam right now, I would use pen for notes in my references just to avoid any potential issue.