A few months ago, there was a TV series called Balderdash & Piffle, presented by Victoria Coren. The point ot the programme was to get members of the public to produce evidence for the scholars at The Oxford English Dictionary (TOED) to show them that certain words had been around earlier than the dictionary claimed. One of the words investigated was '99' for the chocolate ice-cream.
All sorts of claims and counter-claims were made, including one that it was a reference to an elite royal guard in Italy consisting of exactly 99 men! In other words, it was something extra special.
Certainly, the earliest hard evidence for it is in a Cadbury's price-list, theough even that is unclear as to whether it referred only to the chocolate or to an ice-cream with the chocolate in it.
The online edition of TOED still says that the origin is unknown.