If they make them optional too often, fans will start complaining that there are too many useless items. I would be cool if the biggoron sword became required for maybe just one boss.
I think the key is to figure out how to make items optional and useful. The two games in the series that did this best were Legend of Zelda and Ocarina of Time. In Legend of Zelda you could beat the game while only collecting 5 of the 12 dungeon items in the game. Some of those skippable items are infinitely useful like the magic key and magic wand.
Ocarina of Time is very interesting in this regard as well. You could beat the game without ever obtaining deku nuts, magic beans, fire arrows, ice arrows, farore's wind, nayru's love, and the lens of truth. Three of those items are so useful that virtually no one considers skipping them- deku nuts, fire arrows, and the lens of truth. You actually have to find new ways to proceed through puzzles in order to skip the fire arrows (in Ganon's Tower there are two instances in which it seems like you have to have them but you actually don't), and you have to memorize certain parts of the game to skip the lens of truth. Not to mention you could beat the game while skipping several of the equipment items as well. Besides the obvious biggoron sword you could skip the hylian shield and both elemental tunics. If you're looking for a challenge, try skipping the goron tunic- you need fairies and/or lots of hearts but you can beat the game without it.
I'd love it if optional items were much more frequent in modern Zelda games. This was something that disappointed me about Skyward Sword. For instance there was a perfect opportunity to allow players to find an alternative method to reach the Fire Sanctuary besides using the Fireshield Earrings. The game designers could have easily allowed players to use a guardian potion plus instead but the game physically prevents players from doing so. I don't see the point of forcing people to find a protective item that's limited to a specific element when an item that grants invincibility is readily available. Why can't we have different solutions to problems like how in Ocarina of Time you can light a torch in four different ways depending on whether you're a child or adult and how you are equipped- deku stick, shooting an arrow through a flame, fire arrow, din's fire?