I have a few ideas why dungeons might be as ironic as they are.
1) Like other members have stated, the "weapons" are usually tools for whoever worshipped or worked in the temple would use to get around. It could be a coincidence that they can be used in the boss room or on the boss itself
2) Dungeons (Temples), Bosses, and new weapons/tools are created by the goddesses, the antagonist, or a third party to see Link grow as a hero, or pest. So it's natural that as Link progresses through the dungeon, that he receives a gift to fight a special enemy left by either of the three groups previously mentioned.
e.g.) In SS, while Ghirahim never really helped Link, he did let Link continue to get stronger. Like in the Ancient Cistern, all Ghirahim does is have Link fight Koloktos, probably aware that there is a sacred flame waiting for Link if he defeated Koloktos.
3) Some bosses weren't supposed to be there in the first place.
-e.g.) In WW, Link receives the grappling hook in Dragon Roost Cavern. It was a tool used by the Ruto before they could fly. Around the same time, Link learns from Medli that a monster (distant relative of Gohma) was causing all the turbulence with Lord Valoo. In my opinion, Ganon placed Gohma inside that chamber below Valoo. Although Dragon Roost Cavern isn't the traditional dungeon, it explains the somewhat ironic concept of dungeons.
That's all I have to say.