Yes this is maybe possible... In the other hand when we think about SECONDARY MODE, it is clear that the other stack of arrows should have some big disadvantages. Just like many melee weapons do. Poleaxe does less damage and is slower when the blunt option is used, even if it doesn't make sense that the same weapon is slower and does worse damage in blunt mode. It is a balance issue and solved like that..
Same should apply to arrows. You take two stacks of arrows, one is main stack and another is secondary. Always when using the secondary one your bow draws slowly and it does less damage. This is tricky thing to balance. Not that simple but doable with some tweaking.
I don't think you can compare those two things.
The secondary mode of halberds contains blunt damage, instead of cutting damage, which makes is much more useful against armored targets (which, I would say, is the majority of targets and infantryman has to deal with), and it would get knockdown. So to prevent half of the server lying around on the battlefield due to drastically increased amounts of long, fast and hart hitting blunt weapons, you have to make the secondary mode inferior to the primary mode.
Concerning arrows things are totally different!
I don't know how the current system works, concerning which of your different quivers counts when, but in the case of archers (and crossbowmen) the weapon and the ammunition are
two different items, and you pay with weight, slots and upkeep for your ammunition. If you use better ammunition you pay it with even more upkeep and with fewer shots.
So in my eyes, it doesn't matter at all, if someone is using two big stacks of cheap ammunition, two small stacks of expensive ammunition, or one big stack of cheap and one small stack of expensive ammunition. It is already balanced by the different values for upkeep and shots.
I don't see any reason why you should get punished for switching between the items you have equipped. It's like saying "If a shieldman switches from his sword to his hammer to fight a tincan, the hammer should have lowered damage, because he already has a sword"... eeerrr wut?