I'll quickly jump in this thread to emphasize that "stun" or "crowd-control" actions have always existed, even in fast-action games.
If you ever play any MOBA, you'll see that those 2 seconds slow / stun are seemingly endless in your eyes
I'm not against a heavy gameplay balance approche for such a powerful tool as an EMP. If the EMP originates from the ship, dropping its own shield is perhaps a good compromise.
Besides, let's not forget that EMP blast hits everyone, your allies included. This is already a very potent counter-balance by itself
As for the UI twitch when hit by an EMP, that's fine by me. Deus Ex have made nice UI effects for that kind of action.
So we may consider 2 different outcomes for a EMP discharge: either drain a shield's portion of ships within range, or if that ship has already no shield, make it "stunned" for a few seconds.