From the Slytherin Welcome Message:
We also get respect from our fellow students. Yes, some of that respect might be tinged with fear, because of our Dark reputation, but you know what? It can be fun, having a reputation for walking on the wild side. Chuck out a few hints that you’ve got access to a whole library of curses, and see whether anyone feels like nicking your pencil case.
I was always under the impression that everyone at Hogwarts wrote with ink and quills, so why would they need something to hold pencils?
Does anyone at Hogwarts ever use pencils or pens to write with?

ctrl fin all of the books - "pencil" is only mentioned in 4 books, not once is anyone using a pencil to write. on some occasions it's "pencil-case", on some it's Rita Skeeter's pencilled eyebrows, and once it's "pencil-like object", meaning wand. – Gallifreyan Aug 01 '17 at 19:00