I feel like the ammo aspect is a big part of what makes the game challenging. Like others have said, you can always get more ammo by using the opposite beam (i.e. killing enemies with the light beam gives dark beam ammo and vice versa), and you can also use the charge beam for a free shot even with 0 ammo.
All of that put together can lead to some of the most exciting boss battles where you’re out or almost out of ammo but still have a chance to get the final blow in before they do. Infinite ammo wouldn’t necessarily ruin the game overall in my opinion, exploring would still be fun and exciting. But it would certainly rob you of those exciting moments.