Eva plunges into the A.T. Field's violent interference waves with both hands.
Dr. Nick:: *restrains himself from making a Goatse-related joke*
Reichu: While most screenshots indicate that the Evas' caretakers keep their fingernail length nicely in check, every once in a while an animator will draw them with these creepy long nails, as you can see here…
The Evas seem to use their hands as "focal points" when they work their ATF magic, perhaps akin to how traditional wizards use wands and staffs. If you cut an Eva's hands off, presumably she'll still be able to rip through an opponent's ATF-shield; hands just make things easier.