Eh. I think about Pokéballs because they’re so unmissably integral to how the setting works. How Pokéballs function has massive implications for the way Pokémon interact with humans, so I can’t really avoid the damn things. Other items, not so much.
I think a lot of those type-boosting items are probably viewed as either confidence boosters of some sort (the scarf, the Hard Stone, maybe the Charcoal), as directly increasing the potency of attacks in some way (the Poison Barb, possibly the Magnet) or as being actually magical – it’s a common belief, for instance, that the body parts of magical creatures are magical as well, and Dragon Pokémon are ridiculously magical, so one of their fangs could very well have some sort of talismanic properties; we’re probably supposed to imagine something similar regarding the Mystic Water pendant.
I suppose some of the others might have special properties because they’re made of materials unavailable in the real world, for instance, the glass in Choice Specs is made from the ground-up core of a Starmie and bends the light in such a way as to reveal the points of a Pokémon’s body most vulnerable to magical attacks, or a Choice Scarf is made from… I don’t know, like, an Alakazam’s moustache hair or something.
The sixteen Plates, which determine Arceus’ nature and powers, are probably important, but goodness knows how they work. In… *ahem*… that movie… Arceus is able to use all of the Plates he possesses at once, changing his type at will in order to block incoming attacks. I think the way we’re supposed to see it is that Arceus, in his natural state, belongs to all types, but is in a weakened and diminished form without the Plates, which contain a portion of his ‘essence’ and can be used as a source of power either by him or by any other Pokémon.
So, yeah. The answer is that for most items I don’t have a clue; don’t even ask about evolution stones (and don’t say ‘radiation’ because that isn’t an answer; that’s just more questions).
Pokémaniacal 