However small Susan's shrunk them, it's at least enough to fit eight of them in that box. Don't worry, though, it's got air holes.
And THIS is something I've been wanting to have happen since before I even got around to the potions, and the main reason I included shrink potions. Granted, this is me, I probably would have included them anyway, BUT, from a STORY perspective, this is how Susan is dealing with human opponents.
As for where she's storing all those potions, it's video game logic. Wherever those potions are, there's also a bunch of gold, outfits, and whatever else she might be carrying, and she can summon them from anywhere.
Of course, that wasn't good enough for the third Fable game, so when you paused it, you got magically transported to another location entirely where everything was stored and you had to walk around to them, because REALISM!