Maybe the question should be, what makes one yoyo better (and, thus, more desirable and more expensive secondhand) than another? But, the answer to that is actually pretty involved... High end, competition level yoyos these days are all basically around the same price, with the exception of Japanese yoyos, which are almost double. I don't know why it's that way, except that Japanese yoyos play really, really well.
The secondhand market is another story though.
To use the yoyo I mentioned earlier (The Peak, in case you're wondering), it was liked by basically everybody. It was made by a boutique company and, at the time, they were a super, super small operation. So, they didn't make too many. Routinely, when new Peaks would drop, the servers at the site that sold them would crash from the traffic. So, they were always hard to get firsthand. People liked them, so they rarely showed up in the used market. Then, they stopped making them in 2010 and people are still in a frenzy and will offer stupid amounts of money to get their hands on a Peak. But yeah, there probably aren't more than like 15 or so of each color of Peak, so that has something to do with it. I've heard about people actually paying like $600 for used Peaks. Bananas.
It's like cars I guess. They all do basically the same thing, but countless variables make some worth more than others.
It's funny... Initially, I was happy that yoyoing was a lot cheaper than arcade stuff. But, yeah... That's not true at all after a certain point.