In my experience, shade is better under AI control in a fleet context, since it will consistently act as effective PD and do some damage/emp to enemy ships. Afflictor is better as a player ship for strike purposes, but in AI hands, it is much less effective. In general (IMO), you can't depend on the AI to use alpha strike abilities effectively, but you can depend on it to use EMP fairly effectively. I would rather have AI shades in my fleet but I would also rather pilot an afflictor. In general, I don't use either much because tempests are better, except maybe one afflictor until I get a capital ship.
I would also say that EMP is more valuable in a fleet context than in a solo fight, especially when equipped on smaller ships. A wolf EMPing a capital/cruiser with an ion beam is much more value than any amount of damage it could do with a pulse laser in a reasonable amount of time, but in a solo fight, a wolf with an ion beam is going to be much less effective than one with a pulse laser since it lacks finishing power. Analyzing ships in solo fights can miss the bigger picture.