Hm... in champion select, you want to counterpick, but... If I recall correctly, assassins are useless if not fed because of their poor farming ability. The best thing I can think of is every time Akali comes close to take cs, you poke her. You don't go ham, hoping to kill her, you poke her down and play a bit passively until it's time. A good jungler ganks Akali often, because she's next to useless when underfed, so consider that.
Assassins don't have as good waveclear and cs as mages (not that they can't, but it's not as good), so one idea is to out-farm her without taking damage as much as possible (remember, 18 cs = 1 kill or so). Then build a mix of offense and defense, denying her those much needed kills. As long as everyone is warding properly, she shouldn't be able to get free kills at bot lane if she's desperate enough to try.
One great counter against Zed and Akali is silver sash. Seriously, that item almost as core as Zhonya's, plus it gives magic resist.