Zappa's music is owned by the Zappa family trust and it is marketed by Ryko.
Either the Ryko contract is up for re-negotiation or there has been some sort of disagreement between the ZFT and Ryko. The ZFT is run by Gail Zappa, maybe they are planning a wholesale re-issue of re-masterd Zappa music, who knows?
Either way Zappa CD's are pretty much unobtainable at the moment from the usual sources, hence the stupid prices being asked.
As for Zappa's music appearing on Spotify. There are probably two chances. Fat and None.
Sorry David, I must be missing something. I can't find any reference to Zappa in any of your links.
That FAQ link is more a general example as to why some artists might not be available, rather than relating particularly to Zappa. In the meantime, why not check out ZappaRadio over on the Zappa website?