Currently my players can make a HyperConomy shop anywhere they like, even if they don't have build permissions. In a situation where players are encouraged to purchase land this is undesireable.

Please add the option to have shop regions honor WorldGuard regions and not allow players to create a shop if they don't have build permissions.

You could try the Region Specific Permissions plugin:
http://dev.bukkit.org/bukkit-plugins/rsp-region-specific-permissions/

I can look into this. I already have plans to make regions in hyperconomy which limit where shops can be built.