I have discussed many of the issues you raise in other posts, but I'll summarise my thoughts here, if you don't mind?
1) It should be possible to ban certain resources. After all, as you point out, whales and ivory were once harvested without legal restraint, and cocaine and other opiates were commonly used in 'polite society', yet not anymore.
2) Banning a resource might be done for several major reasons. a) A hostile civ has a lot of that resource, and you want to ban it as a prelude to getting other nations to ban it, too-thus denying your enemy a market for his product. b) You might want to prevent a hostile civ from gaining access to a vital strategic resource-either from other civs or from your own private sector. c) You want to ban a resource so that you can 'make a killing' by trading the resource as contraband.
3) Contraband resources are resources that have been banned, but which are traded anyway. Contraband requires a 'black market' Small Wonder, and these resources can be traded to friend and enemy alike-for much more than you could get from it legally! In addition, contraband resources cause increased crime and corruption in the recipient nation.
4) Like you, I feel that increasing techs should allow regular improvements in your terrain improvements. So, for instance, farms and mines get better at least once per age. Though you would have to pay to upgrade them!
Anyway, hope that helps

!
Yours,
Aussie_Lurker.