It will be fine.
With the ability to sell more at once will make things cheaper. If you wish to buy fewer at once, it will cost more. Welcome to the real world.
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Unfortunately, I am not sure most of the player base even cares about "real world" economics. Most of them just look at the lowest going price and undercut it by 1-5 gil, regardless of the stack size. While I do think it would be nice to be able to purchase the amount I want (eg. stack of 99 is on the market, I only need 10-routinely annoying, but I just go gather it myself usually), it will no doubt slow selling of things.
And yet we still do not have stackable maps... :(
LOL True story. However, the last interview seemed to focus more on cost of development. Many times they referenced "We will have to see what it would cost to implement this" So it went from, it will crash the server to it's going to cost too much money to develop. Which, I thought was a little concerning.