Many thanks for the replies. I'll keep them as vertical as possible, upside down in the bag but tip down when against my wall.
I put a little paint symbol on the bottom of my hilt of the bokken and on the end of the jo (for identification). Its a very obvious place and they've been there for 10 years and haven't worn off. However I would recognise the weapons now by their scratches and dents!
I also have a very strange jo (which I no longer use) which I mistakenly bought when I started aikido. I remember them telling me it was Japanese bamboo. Its definately bamboo, but it is solid (no hole). It is as light as anything (like its made out of polystyrene) and bends like a bow. It got very dented from too much kumijo, but is quite springy for jo taking. Also impressive for jo suburi 'cos you can do it amazingly fast (but it is so light you don't actually get any muscle memory)!