Conquest Status *does* affect spell availability in spell shops. One example I've seen proof of is this. Drain. Drain is a quest only spell (the quest in San d'Oria) except when Windhurst is Rank #1 Overall (checkable on your "region map"). When Windhurst has Rank #1 Overall, Drain is available from the Port magic shop, but at no other time (meaning Rank #2 = no Drain, Rank #3 = no Drain).
That's the only one I *know* to be true. I was talking on the phone to a friend of mine on a different server, he bought drain from the Windhurst shop (he was also *from* Windhurst). I happily (on my server, where Windhurst is in last place for conquest) hiked over to Windhurst at level 17, dodging this, that, and the other, and was all excited to get Drain. It was a wasted walk. I later found out that it was due to the Conquest Rank. I called my friend, he checked it, and sure enough, Windhurst was #1 on his server, and sold drain, but on my server, it was #3 and did not. A week later, Windhurst was Rank 2 on his server and no longer sold Drain.