I bet you an official English translation and release of Mother 3 that the people selling copies on eBay did not pay anywhere near the amounts they are asking.
Mind you, if you're lazy and only look on eBay for rare games you deserve to get ripped off.
As was said though, the prices that things sell for are what people are willing to pay for them. If people didn't want to pay them, they wouldn't sell. And, sure, some of the people selling it on there are people who got it from someone else's mother who was selling all of her son's games at a tag sale for $20 for the lot of them, but, obviously not taking the time to go around to tag sales and flea markets and such and just hopping on eBay is the choice that some people make, and that's what they're willing to pay to not have to do that.
For instance, the price on it has come down significantly since when the SNES version was the only option, but, despite there being a Wii VC, PS1, DS, and iOS port/remake/version of Chrono Trigger, the cheapest Buy it Now for the SNES Chrono Trigger currently on eBay is still $70 (one with stickers all over it). Granted it's possible to get it much cheaper than that by waiting for a regular auction to end (one sold for $25, one for $30, one for $35, and then more in the $40-50 range), but, given the various options that are much cheaper, obviously there are still people who just want to own the original version.
Anyway though, that was a bit of an aside, but, my main point was, sure, the price of Earthbound will come down is other versions of it are released here, but it's not like all of a sudden all the people selling it are going to be like, "Oh well, guess the jig is up! Darn!" and sell them all for $10 or something. There's still going to be demand for the original version as well.