It seems to mainly be a balance issue. Lets use Stake Launcher using arrows for example.
Stakes have 25 damage, the highest damage arrow (Venom) has 17. So if you adjust the Stake Launcher accordingly to have the damage output required to compensate for the 8 lost damage it would have a base damage of 83 instead of 75.
That doesn't seem so bad right? Well, every other arrow type is obviously useless, since the best damage comes from using Venom (just like the Pulse Bow). Even if you make your own arrows out of stone and wood, a stack of 35 Venom arrows takes a Vile of Venom that costs 10s. A stack of 35 Stakes costs 5s 25c. So you get the same amount of ammunition for almost half the price (more than half if you buy arrows instead of making them).
By making a different ammo type instead of just using arrows, they allow you to achieve the designated (balanced) damage output for a much cheaper price. I would much rather have two stacks of Stakes than one stack of Venom arrows.
You also don't need to carry around every single weapon using every single ammo type. Every weapon has a different use, and you don't need all of them at all times. Designate the 2-4 you may use before you go do what you plan to do; boss fight, event, whatever; and only take them. You can switch when you port back home to do something else.