Frame challenge: Do you need an explanation?
When fruits are consistently the only objects being weaponized in your fictional universe, and the overall tone of the work is wacky enough that the audience knows that it is not to be taken too seriously, then they are going to suspend their disbelieve and just accept that this is how your world works.
You can easily make up a flimsy concept like "fruit power" which is inherit in all fruits and makes them powerful weapons. Other weapons like firearms or bladed weapons lack "fruit power", making them inherently inferior to fruit-based weaponry and thus an illogical choice of weapon in your world. What is that "fruit power"? Where does it come from? Nobody knows and nobody cares. It's inherent in your world, and that's all that matters.
The "everything needs a scientifically valid explanation" mindset is a common trap new worldbuilders fall into. As long as a world is internally consistent, it doesn't matter that the scenario would not make much sense in our world. The urge to come up with a plausible explanation for everything that's special about your world can be distracting and limiting.
This is even more true in the context of video games, where players will gladly accept the most unrealistic properties of the world as long as they are reflected in the games mechanics.
Should European pears (Pyrus communis) or Asian pears (Pyrus pyrifolia) be preferred?
In the context of a video game, I would prefer European pears for a simple UI reason: Asian pears are too easy to mistake for apples. Making objects distinct by color alone is dangerous due to color blindness. So when it is important for the player to tell apples and pears apart, then you should give them different shapes.