Couldn't the PC itself be a huge money sink?
Also, just because an item is used a lot in the current game, doesn't mean it always needs to be that way. A growable cheap alternative to ethers has already got enough use as it is. Why attempt to increase the market value of a very specific item that can easily be replaced? I understand MMO's have an economy, and that every change needs to be thoroughly thought out before implementation, but I still don't think adding it to the game would be that much of an issue.
Most late game players just grind using Pay Day and stock up on hundreds of potions, and probably ethers too if leppas weren't easier to obtain,
from PokeMarts, which has no real impact on the economy, same goes for repels.
Useful items will always have a use, secret bases aren't everywhere, such as underwater, in dungeons, other regions, and even in a lot of routes.
These places will still require players to stock up on items if needed, most of these items aren't even connected to the in game economy.
Plus with the future inclusion of things like raids/new dungeons, those items will see even more usage.
And actually, adding another large money sink, like ocarinas would probably balance out some of the fluctuations. Or you could even make healing at a secret base cost something to de-incentivize using them too much.
Shiny's will always be worth a lot, 1/30000 chance is a crazy high number and easier access to horde farming more than likely wouldn't change the market value substantially enough to notice a difference.
Players have been wanting this feature since the game came out, and during my research I still haven't found a good enough reason to convince me why it shouldn't be in the game.
At the very least, add something to secret bases to make them more useful other than contests on occasion. Quality of life changes are also a huge part of MMOs after all. Sometimes convenience needs to outweigh the grind, esp. late game.