Pretty much everyone likes empty bottles in Zelda, but in real life (at least in relatively well-off societies) not so much. Empty bottles are just thrown into the garbage...err...recycle bin. Don't copy off Link here.
It's a sign of the times, in the game's timeline getting an empty bottle to put your potions in is very rare. In the modern timeline you can buy any potion you want which is already packaged in which they are single use only. Myself, I keep a bottle on me and use it as much as I can.