Under the description of named bullet it lists (will save negates, harmless object) and spell resistance yes (harmless object)
I read this to be like the spell magic weapon--ie that those are applied when you are casting on the weapon or piece of ammunition--NOT that the target gets a will save. I know the specific description later states that you must overcome the targets SR when you hit, but it does not get a will save does it?
Otherwise everytime you hit something with a weapon with magic weapon on it (such as a constructed magic weapon) the target would get a will save to not have your weapon be magic.
The target of the named bullet does not get a will save.
The will save and SR in the effects section applies to the targetted ammunition/thrown weapon, not the person you attack (in the exact same way as Magic Weapon as you say).
You are right that this type of spell would not normally need to overcome SR. That's why they need to specify it in the body of the description. If it also allowed a will save it would be called out in the same way.