Link isn't using his rupees as arrowheads.
Rather, the shops actually all sell arrows individually at one arrow per Rupee, but rather than making you go in and out of the shop over and over again to refill your supply, the game just automatically deducts the one rupee every time you shoot, which represents Link not being able to use that rupee for anything else since he has to buy an arrow instead. Link is using his rupees as arrowheads.
They're hard, can hold an edge, and might well be the best arrowhead material he can find. Aside from using them at the few shops, rupees (especially the 1-value yellow ones, which he makes change for when he can) are otherwise Worthless Yellow Rocks to him. The monsters and bosses aren't only guarding the pieces of Tri-Force, they're trying to break in.
The Dungeons weren't originally evil, they were just places of safety that Zelda somehow created with the Tri-Force of Wisdom. They had puzzles, sure; but just to prevent Ganon from getting to it. But Darkness has a way of seeping in, and they slipped through the doors and walls. But they can't get into the final Tri-Force chamber, so they hold the fort until they can break through or Ganon manifests enough to do it himself.Link's bright soul and killing the boss shows the piece that he's worthy, and it lets him in.
Ganon is actually Yuga.
This far down the timeline, it can generally be assumed that Ganon has become a mindless raging beast of hatred. However, it is also theorized that he had a hand in Zelda II's backstory, implying that he's still smarter than he seems at this point. Considering that the last we saw of Yuga in A Link Between Worlds was him merged with Ganon, it is possible that merger is still holding up, especially since these two games are placed near each other on the timeline. One piece of Zelda 1 artwork even depicts Ganon with white skin, just like he had with Yuga. Hyrule's Golden Goddesses religion got Hijacked by Jesus.
This Link isn't originally from Hyrule.
This is how the non-canon Valiant Comics adaptations play it. But to go further, this Link is not only not from Hyrule, he doesn't speak Hylian natively; which language and which translation you play decides how fluent he is, ranging from nearly-native in the original Japanese to barely understanding anyone (possibly with a lot of false cognates and false friends) in the original English release. The screen where the White Sword is found is Ploymus Mountain.
It's atop a waterfall in a river inhabited by Zoras, and guarded by a lone Lynel which the game's designers no doubt expected you to sneak around and avoid combat, especially in your first playthrough or two.