The biggest difference between the iPod 1st gen. and the 2nd gen. would be the fact that the second generation has a hardware upgrade as well as a built in speaker. As far as hacking, it's a bit different path to hacking it but they both still have a untethered hack released for them.
As far as compatibility regarding the 1st and 2nd...I don't think any information is really floating around about that. I think most application still work for both but don't take my word for it. And I don't believe that is just some code in the .ipa that's reserved for compatibility. The application is built for certain platforms. Unless you reverse engineer the application... I think u would need to stick to whatever you can get.
(The second paragraph is merely speculation. It's not 100% true. If you or anybody else has more information on the subject matter, please do us all a favor and post it)