As for the "content": Everything within the game is part of its content. Dungeons, enemies, bushes, chests, mountains and so on, whatever it may be. To me this isn't even a matter of opinions, it's just fact that it's content within the game.
So yes, items are clearly content to the game. Even with all 100% runs for all games, you never do everything within the game and you usually don't obtain everything you can either. I've never heard of such category where you do everything you possibly can to fully show/do the game's "content".
For ALttP 100%, this is the "Glitched" category, where you may use what the game has to offer to accomplish the 100% definition. This will clearly skip parts of the game, yes, because that's what you are supposed to do in a speedrun in general: Accomplish the goal, skip anything that you don't need or is slower to do. You'll see that the 100% record for "No Major Glitches" also skips a lot of content:
https://www.speedrun.com/alttp/run/8y8p2k1z
But yes, dungeons and bosses are part of the content, you are correct.
Raja!
