Why so many JL Audio Fathom subs for sale I wonder

Simple... Its because the new V2's of the Fathom & Gotham have been released.

rossman: Bingo

I have a pair of 110s and have had trouble with one.  Second, the high gloss black finish is very finicky!  Shows every touch and cannot be easily polished up.   I run the pair as Master/Satellite, so there's only one source of low frequency information played through both. 

First of all it is a very popular sub. People who try to integrate one sub are frequently frustrated with the results and eventually give up so their subs show up on the used market. People have to understand that one sub just will not do it. Trying to stick with one to save money will not work. You have to get into subs knowing that you are going to need at least two in the end maybe more depending on your system. JL Audio subs are representative of the upper mid fi of the market. There are just a few manufactured subs out there that are significantly superior and they are very expensive. The Gotham is right up there with the best of them.
Anyway, integrating subs correctly is not easy or simple endeavor. If you start getting frustrated try and find someone with some experience to help out. The only reason to use one sub is knowing that you will have to get a second one down the line. In the meanwhile if you can scarf up a used JL Audio sub at a good price go for it.  

They are a high quality, popular subwoofer but adding subwoofers to a system can cause disillusionment.