The current 'icon-less' abilities in the game work by referencing a blank icon. They still take up a slot on the UI, even though you don't see it. The game code requires a UI slot to be used to field an ability. Currently the stuff that tells the game engine how many slots it has at it's disposal is hard-coded.

Check out the scout abilities, like immune to phase jump degradation and the Advent scout lingering presence ability (It's called 'spying attacks' in the entity files). You'll see what we mean.