Well, that answers the question whether it's a bug - it is not. It still remains open whether bonuses should stack, unless I'm missing something?
Right now, it seems far, far easier to split something like this Nepotism into two bonuses, one that can be stacked (heh) and doesn't give a stat bonus, and one that cannot and does give that intended-to-be-nonstackable bonus... than it is to manually create differently named and thus stackable bonuses by item/enemy names for all the gazillion weapons/enemies around, one by one. Which is the one way I can see the current state of the game allowing stacking weapon bonuses, and I don't think any big mod is going to go with that.