I didn't do it, but I might very well have if I hadn't used a walkthrough.
The thing is, not everyone finds the Old Man's Letter. If you were trying to play the game without one, there's every chance that you might think that's the only way to get a potion. If you know the hidden secret and that you can get a Red Potion for 80 (or was it more?) rupees, then you know it's a bad deal. But if you haven't found the hidden shop, and you think it's a choice between having an item that will revive you twice if you die, or a chance to last longer without dying, it's a much tougher choice.
In fact, it's possible that those particular shops were put there for testing purposes, and they never actually intended players to find it (development teams were a lot more haphazard back then, willing to leave Easter eggs behind for those few who knew where to look). So the game may have originally offered no way to purchase potions, and in that case the choice would make more sense. They stopped doing things like that when they realized that if enough people have the game, everything in it will eventually be uncovered and made public, no matter how cleverly they think they've hidden it.
Either that, or the choice itself was really just there for those players that somehow miss the Letter. Not sure...
Another possibility is that the potion shops were deliberately added on (or left in) at the last minute to reduce the overall difficulty of the game because they decided it was too hard as designed.
In any case, I'm sure it wasn't intended to be such a poor deal, it just ended up being that way.