I was told it's because the flake in a 99 is 99mm long.

I dont know when but I thought is was because they cost 99 pence

Two more 'answers' to add to the mix; it's like "call my bluff"; **The name 99 for the short Flake dates back to its launch in 1930 when the UK ice-cream industry was dominated by Italians. Legend had it that a King of Italy surrounded himself with an elite bodyguard of 99 soldiers. Therefore, to Italians, the number 99 signified the very finest quality. ** '99flake' quite simply it is order no. 99 on the cadbury rps product list and was the 99th. product introduced by cadbury.**

Unsure of the details but in 1899 in vienna/italy???? there was a war and an ice cream maker decided to commemorate the soldiers who died (they wore feathers in their hats so when they went over the top of the trenches the 99 is supposed to look similar)

Maybe it's called "99" because there seem to be 99 reasons why it's called that?