Two things (both previously stated).
1) Stake Launcher has a static damage output. 75 from the weapon, 25 from stakes (100 overall). Altering the weapon damage to 83 to match the 17 damage from Venom arrows keeps the 100, but it still isn't static damage. Why? Cause other less effective arrows could also be used, making damage output lower than intended for the weapon.
2) A stack of Venom arrows takes about twice as much money as a stack of stakes. Why change the game to require twice as much money to achieve the same damage?
The Pulse Bow is suppose to have that fluctuating damage based on the arrow used. It pierces/bounces regardless, but if you want higher damage you have to spend more money. The Stake Launcher is not meant for that same fluctuating damage.
Also, another balance mechanic is the Stake Launcher is not affected by Archery Potions, even though Shroomite Armor considers it an arrow based weapon. You would have to take that into account when balancing it as well, as using arrows for its ammo would then let the Archery Potions work.