My last stint in Afghanistan was winter '09/'10. I had a Peterson 80s and two basket briars. I was worried about customs also, but they didn't even bat an eye at them. I also had them in my carry on. You have to remember that hookas get a bad rap from the pot crowd.
As for tobacco, take what ever is tinned up and then plenty of ziplock baggies to keep open tins in. That will help keep it fresh. Also, I would set yourself up a "care package" for someone to send over to you a soon as you get there and get a solid address, so you can have a quick resupply. Then you can order from say smokingpipes.com, 4noggins, or pipesandcigars.
As for buying anything over there, I wouldn't count on that. I don't know where you are going to be, but the Afghans where I was (Marjeh) couldn't understand that it was just tobacco in my pipe. Plus I doubt the PX will have anything, that is if you are somewhere with a PX. The PX truck definitely won't have anything.
While I was there I tried a lot of different Peterson Blends while I was there. I liked those tins because I could throw a can, in a baggy, and then in my pack for foot patrols. Also, I found that Oakley hard cases for say M Frames or Half Jackets fit a pipe, cleaners, tool, and a ziplock with a day or two worth of tobacco fits nicely when you rip out the foam.
Also, you could take some briars and then right be for you leave mail them home. Just a suggestion.
Have a good tour and return home safely.