I don't know why they're expensive now. When they first came out, I bought it for like $150 since that was the original price. However, about 4 or 5 years ago, I picked up a couple more Pros, one brand new for like $5 and one used one for like $1 (actually Y100). Seems like they are expensive now simply because it's requirement for some IMO cool games.
I might be able to shed some light on why they were that expensive back in the day. The Arcade Card Pro/Duo was scheduled to come out in '93 around Dec. Of course the magazines made a big deal out of it since Hudson and SNK partnered up in order to get Fatal Fury 2/SP, etc on PCE. The original release dates were late '93. However, sometime before that (a couple of months before probably), there was a RAM chip shortage. Not sure on the details, but basically the shortage caused release date to slip to Mar '94. I'm guessing the final price was higher than originally thought due to the shortage of chips at the time. All I remember for sure was I was glad they delayed it because I was saving up money like crazy just to buy it.
Finally, they released two versions of the card in order to support regular CD hardware (original model) and SCD hardware (Duo etc). AC capability requires Syscard 3 BIOS and of course having it on the AC card for Duo users is redundant. This made the AC Duo about $20 cheaper than Pro. The first articles/ads about the arcade card talked about some 2in1 adapter where you'd plug the Duo and the Sys Card 3 into the adapter and then the whole thing into the "old" CDROM system. That was obviously scrapped in favor of syscard3 + AC all in one model, which became the AC Pro.
Honestly, I don't see why it's expensive at all. I guess it's just the price of admission. As a matter of fact, outside of Sapphire and perhaps Madou Monogatari, the AC only games seem to be very common and cheap. Hell, in '99, a store in Akihabara was selling brand new copies of Fatal Fury 2 for Y50 (50 cents). They were obviously clearing out old dead stock but that game is pretty much worthless now (there are other reasons as well). Yet it's a nice game to show off the PCE.