As far as I can tell, by the rules, there is no set limit --
anything in your pack (be it potions or other) can be retrived with the same minor action. So I would think as long as your pack has the space capacity for it and you aren't at max load, then you're "good to go" by the plain rules. That is in line with the concept of reducing the micromanaging.
If it does approach ridiculous levels, your only recourse (by the rules) that I can see is to monitor capacity on the backpack (they have to start emptying out other gear after a while) and/or load capacity would slow them down. Of course, that will just lead to the player in question wanting to get a bag of holding or similar.
If you're willing to go to "DM say-so" then there could be added dangers -- if you have a pack full of vials, whenever you take falling damage, there is some chance that a vial or two breaks.
Or the town doesn't have any more components to sell since the PCs have bought it all from the mass potion making!
Having said that, I (personally) find 5 to be a reasonable number after which it starts to seem kind of silly. If in the middle of combat you have only a faction of your turn (ie a minor action) to reach in your pack and grab just the right vial .... it just starts to seem silly after a bit.
Incidently, there is a belt (called potion belt or something like that - it's in AV2) that lets you store 6 potions at your waist that can be removed as a free action. So, yeah, if has the potential to get out of hand fast if you have players who (rightfully or wrongfully) just want to stock up on mass potion production ...
As for being able to create 1 potion a day as a house rule: it's a simple enough rule that's easy to remember, so if you want/need to slow down the potential mass production, sure, go for it.