In the MC a Minish says, and I quote:
"You've heard of travellers who find a Kinstone and get really lucky? Well, that's all thanks to items made by us Minish! You see, we thrive on making humans happy. It gives us energy. But we only do it in secret."
Another Minish says:
"Sometimes it's a flower seed, and sometimes it's a stone. We hide our lucky items in all sorts of unexpected places. But the real trick is making it tough for humans to notice!"
Both of these quotes gives us evidence to support that it is infact the Minish who hide the items such as hearts, rupees, arrows, bombs, and in MC Kinstones. Another piece of evidence for this, is that after unlocking them, you can find the Remote Bombs in the wild. This doesn't sound like much, but the Remote Bombs were engineered by a Minish and humans do not yet have them. Only the Minish do. This suggests it must be the Minish who hide the items as they are the only ones to have the Remote Bombs to hide.
The final piece of evidence I have to suggest it was the Minish who put the Rupees and other such items in the ground is, Picolyte. For those of you who do not know, Picolyte is a substance which when drunk, gives the drinker increased luck making it easier for him to find a certain type of item. For example, there are types of Picolyte for Rupees, Hearts, Kinstone Pieces and Items (Bombs and Arrows) and some others. Now, Picolyte was engineered, again, by the Minish. Now to me, this is another reason to suggest it was the Minish who put the Rupees and items there in the first place, as they have engineered a 'potion' or 'charm' that makes it easier for humans to find the items.
Also, Rupees are an Indian currency as everyone else has stated. The video provided above proves that it was originally intended to be Rupies. Perhaps Nintendo just liked the name. One thing, is the name of the Indian Currency spelt Rupees or Rupies?