I don't think it was too hard to find Rupees in SS. It was somewhat, but I think this slight difficulty was magnified by the fact that wallet upgrades were easily acquired in SS. When there's more room in your wallet, you want to fill it all up, and it's harder to do. In a game like OoT, where you have a 99- or 200-Rupee wallet, the Rupees falsely appear more abundant because your wallet is filled to the brim more often and any Rupees you find can't be keeped. But then in SS, you are generally able to keep all the Rupees you find, so you want them more, making them seem harder to find.
Also, in SS, there's more to spend your Rupees on. The upgrade system and just the sheer fact that there was more items to purchase emptied out your wallet more often, and made having Rupees a bit more of a necessity. If you wanted to buy one or more of the plethora of items, it was imperative to collect Rupees, which made collecting Rupees seem a bit tedious, and thus made it seem as if finding Rupees harder; and also, with the aforementioned added wallet space, items generally cost more in SS, so more Rupees needed to be collected.
Overall, Rupees were just as easy to find in SS, in my opinion, but they were made more of a necessity and carried a false sense of rarity.