1) apt-get in itself does and will still work. That isnt going away. To the best of my knowledge, you can even still do apt-get update/upgrade to update your packages on touch. However for easier deployment, we now use click packages to deploy apps to touch.

2) will native apps run on touch? Well that depends. When you mean apps with a GUI then no, most likely not. When they haven’t been built using the Qt/QML sdk for Ubuntu, they wont be environmentally aware enough to function on touch. (Though theoretically you could build an app in (say) C++ without the sdk that would work on touch. It would just be an enormously complicated task)

So no: GUI-apps for Desktop Ubuntu in reality just will not run on Touch. The basic difference between Touch and Desktop Ubuntu (at the moment) is that Desktop uses the X display server. All Desktop GUI programs rely on X to render them to screen. Touch does not now and will not have X. A new display server called Mir has been designed for Touch. That brings great advantages compared to X but that means that applications that need X, just will not run on Touch. (Again, this is only for the GUI part of an app). Note also that in the near future, Ubuntu Desktop will also get MIR, but with a fallback to X for apps that don´t do MIR.

Most Commandline interface programs (like corkscrew for instance) will have no inherent problem with Touch. (Touch is however still under heavy development so it may not work right now.)

Sorry for the lenghty reply. This is however pretty complicated stuff :)