The NZ bank account numbering system was developed by Databank in the late 1960's so it's been around for a long time. While I am not aware of any suffixes >99 being used, I'd assume they thought the potential was there at the time they implemented the standard.
Furthermore - the intended use of the suffix is not to denote the number of accounts as commonly thought, but rather the type of account. As it turned out, some banks use it incrementally (Generally starting from zero) and others - like credit unions for example - use it to denote the account type. Some banks use a combination of both.
All NZ banks transact data between each other using 3 digit suffixes. Some years ago I was writing software to produce these transaction records and I had to code it to make sure the suffix was padded with a leading zero irrespective of the number entered.
Once a system is in place it's a huge (possibly insurmountable) task to "rock the boat" so I don't see 3 digit suffixes disappearing anytime soon.