I know that ME3 deals extra damage to headshots on organic enemies, which is reasonable since they have their vital squish brain parts up there. But with synthetic enemies like the geth, they could be designed to store their vital components in a more protected area. Do headshots do extra damage to synthetic enemies? Is the damage bonus the same as it is to organics?
Yes, at least to all Geth I tested on. Headshots deal at least twice as much damage to Geth, and sniping them makes their heads asplode.
In Multiplayer, the Mantis IV sniper Rifle fired into the chest of Geth does about half their health (Bronze difficulty). Headshotting Geth with the same sniper rifle kills them instantly, and causes the same head-explosion that Organics exhibit.