Are mission tokens considered Figures for sake of hero abilities?
Mission tokens are not considered figures unless explicitly declared to be by the mission rules. Therefore, the Covert ability would not apply to Pulse Cannons.

From page 20 of the Rules Reference Guide:


  Objects
  
  Objects refer to elements on the map that are not figures. Doors, crates, and terminals are all considered to be objects.
  
  
  Most mission tokens are considered to be objects, unless the mission rules use the token to represent a figure.
  


The Covert ability reads:


  Covert
  
  Hostile figures 4 or more spaces away from you do not have line of sight to you. You do not block line of sight for those figures.


Since Pulse Cannons are represented by Imperial Mission Tokens, and are not explicitly referred to as figures in the Mission Rules, then they are not figures and Covert does not apply to them.