A good idea for answer from: http://us.battle.net/sc2/en/forum/topic/375108203?page=4

The purpose of the number 54 under portraits is simple. It is to inspire curiosity.

A new player coming to the game will see this number and, over time, grow curious. They will wonder what this number means, what it signifies, how it relates to them and what advantage it might give them in the game. They will scour the user guide, the forums, and the internets in search of answers. In so doing, they will gain more knowledge of the game. Eventually they will cease searching for the "meaning of 54", but only after they have exhausted all fonts of information about Starcraft 2. At this point they will be heavily invested in the game and, in addition to being better players, will play it longer.

The number itself may or may not have some inner meaning to the employees who placed it there, but it will never have meaning for us. It is a symbol of the search for enlightenment, and a prod to those who would not seek such on their own.