Since there are only 9 health potions in the game, the heroes could hypothetically buy all the potions before the game even starts. This leaves no potions available to be placed on the map as called for by the quest guide. It doesn't really make sense that buying potions from the shop should take potions out of the dungeon, so how should I handle this? Should I just set aside all the potions that are required by the dungeon first, and put the rest in the shop?

They buy what hey want, and then later it might make them unable to find potions that should be in the dungeon. There's no limit to how many of an item you're allowed to buy or find beyond how many the game came with, but that's a hard limit. If they purchase all of something, that's all there is in the world until they use one up or sell it back so it can magically reappear in the alchemist's shop.

Don't try to think logically about it. Descent isn't a reality simulation, it's a board game.

But really, if they're spending that much money on healing potions before the dungeon begins (or after for that matter), you should win pretty easily anyway. :-)

They should be spending their money on vitality potions, not healing potions.

By RaW, I believe any unavailable potions are simply not placed in the dungeon. I usually replace vitality potions with healing potions if the vitality ones have run out, though. The OL needs some treasures lying around to distract the heroes...

As the others have said, the number of potions (of any type) is limited by the supply provided. If that runs out then no more can be placed on the map, purchased in store or given out by effects like the treasure draws that reward potions. Not until someone drinks one and puts it back, of course.

In my experience, the store supply rarely runs out of any type of potion. If your heroes are really hoarding them to that extent, then they're either wasting their money or not using them when they should be (or both).

I don't know about that. If the heroes get a pile of coins, they're all going to tend to want to go shopping before they die and lose half, and if they've already got decent weapons, it's entirely plausible that each of them will want to buy 3-5 vitality potions at essentially the same time, which can very easily break the bank in a 4-hero game.

I don't think I've ever run out of any other kind of potion, though.