Hello, it's the 2nd Hokage here with an interesting theory.

The Theory

So, we all know that there are three types of energies, fiver if you include chakra. The three main energy types are physical, spiritual and natural. Chakra, being a blend of energies would be the fourth and sage chakra being the fifth. Now, since everything has one form of energy or another, interacting with it would in one way or another effect the chakra system. For example, Human bodies naturally absorb the water of rain through pores on our skin and because natural energy exists in them in the Naruto world, our characters absorb small portions of natural energy whenever a rain drop hit's their skin. The reason it doesn't effect characters to the same degree as when they are intentionally absorbing naturally energy is because it would take millions and millions of drops being absorbed to have even a small effect on that scale. Naturally, the chances of absorbing that many raindrops is very slim. Another well known fact is that when chakra from another source enters the chakra system of a shinobi, it disrupts the flow of chakra and makes it more difficult to build or control chakra. So, theoritically, it is much tougher to use ninjutsu, genjutsu or any other form of chakra manipulation while being pounded by rain unless covered so it is not absorbed.