Elliott,
The system will allow you to number RefNotes up to 999. Further, there is the Suffix next to the number, so you could even have 999-01 through 999-99, or 999-AA to 999-ZZ, whatever you need.
Setting up your Divisions however is just a great way to organize your notes for any size project, so you aren't wading through such a massive list. With divisions, you can go with either a two-digit or three-digit number, for D-99 or D-999. And again there is the suffix. A neat usage of the suffix I've seen is using asterisks to indicate notes that don't have their finalized text or details yet, and just sort of marking up the plan, so like D-21-***
And lastly, there is also the Renumber option when running the schedule, if you'd like the numbers to all be consecutive starting from 1 on each sheet.
--J