Does the Weapon Master damage bonus affect squad ammo effects?
The Weapon Master upgrade in the Combat Mastery Tree adds 40% damage to ammo powers:
For the ammo powers there are upgrades that grant the ammo power also to your squadmates. Do your squad mates also benefit from the bonus that is granted to Shepard by Weapon Master, or does that only affect Shepard him/herself?
Yes, squad members benefit from the weapon master upgrade. Remember though that the squad bonus skill grants squad members that ammo at only 50% effectiveness. Therefore squad members ammo increases by 20%, not 40%.
The Bioware math explanation can be found here.