Do as you wish but all I can say is that I'd treat these bonuses the same as a regular weapon bonus. Holding two +1 short swords doesn't give you a total +2 to hit, it gives you a +1 to hit with each. Each time you cast an attack spell you'd have to choose whether to use the rod's bonus of the staff's bonus.
This. I think RAW allows them to stack, but I have no problem house ruling that in my game, and think any sane DM should do the same.