Why are we assuming the notepads and pens were stolen? Linda worked for the R's, it's entirely possible if PR bought some pads and pens in bulk that she allowed Linda to take some home.
Linda was one of the very first "suspects" that the R's pointed to, because she had a key. Instead of cooperating with the PD and allowing themselves to be questioned in order to be ruled out as suspects, the R's started throwing a lot of people that they knew under the bus. Linda was one of those and she came to resent it. By the time she wrote the book, she was very upset with how she had been treated in the aftermath of JBR's murder.
Initially when interviewed by police, she noted after being shown pictures that the sheets on JBR's bed were not the sheets she had last made the bed up with. She then speculated that JBR must've wet the bed, which of course was a very common occurrence. The blanket was usually on the bed. Whenever JBR wet the bed, PR would immediately change the bedding, and throw the soiled bedding and the blanket into the wash so they wouldn't smell. There was a separate washer and dryer for JBR, something an intruder would not have known. JBR's bedding and her soiled nightwear was pretty much the only laundry that PR did herself. Both the blanket and the nightie were JBR's favorites, although PR tried to downplay the nightie, saying it had no significance. PR's sister and mother spilled the beans that it was her favorite. Barbara Walters pointed out in an interview, that wrapping her in her favorite blanket and having her favorite nightie next to her were something a parent would do, someone who loved her. The basement and in particular the wine cellar room were cold.
Over time, Linda became convinced that PR was the perpetrator. She wasn't the only one. Her comments in the book are speculation based upon her knowledge of how PR did things with regard to JBR's bedding and soiled clothing.
The safe was never used. It was empty. Hardly anyone even knew it was there. Linda was cleared. Even PR at one point, told a police officer that she was "a good, sweet person. She may need the money, but she won't hurt JonBenet". that She loved JBR. She also loved PR but that changed after the murder and when the R's wrote their book and falsely referred to her as a murder suspect.