Good question! The bonuses and penalties stack for the “basic” attack on the weapon (but not for the MP abilities). For example, Fire does +50% to Life enemies and Death does +50% to Life enemies – This will add a 2x multiplier to attacks against enemies who have life as their defense. It also will make water enemies immune to the basic attack (-100%).
I hope this makes sense.
In this version of the game, I think it makes most sense to simply stack shards on the same weapon as that reduces the cost of MP attacks giving you heavy damage against the appropriate enemies (e.g. 2 different weapons will cover 80% of enemies)