Hey, I actually know exactly why. It was a Geneon license that they made before dying, but then Geneon was busy being on deathrow so Funi handled distribution for the series. Funi did the pressing and shipped it out. I believe it only had one, maybe two pressings. It went out of print before 2010, and Funi let the licensing slip since it got kind of messy when Geneon died.
Scalpers started selling their copies at about $130 before even a year passed. For reference, I went to a con in September of '09 and Nanoha season 1 was going for $35. The following year at the same con, no seller had it and online it was over $100 since it has a pretty strong fanbase and copies went quick. I remember because I was pissed I didn't buy it the previous year when I could.
You think Nanoha's price is bad? Check out the
Higurashi boxset, which suffers from the same exact situation of Geneon fallout. A new copy is almost $700 on Amazon.