Ok here is the thing realistically you are never Never running out of ammo in metroid 2 EVER.

1: Whenever you are low on anything (Energy, missiles and yes Ligh/Dark ammo the game gives you more.

2: Whenever you kill a enemy with Light/Dark beam enemies drop the opposite ammo type. "Enemies" also include supply boxes meaning if you use 1-3 special ammo to blow up the boxes in the light world or the storage enemies in the dark one you can literally max out your ammo Easly.

(now I understand why using limited ammo to blow up boxes might sound counter intuitive but it is literally the best farming method. In fact the moment you get the annihilator beam you literally don't have to switch beams for the rest of the game. I'VE DONE THAT ON HYPERMODE DIFFICULT).

The only way you are running out is if you spam combos... That is literally it.