I am currently using nautilus actions, an application that lets one add useful commands to the context menu, will something as useful be included in the Unity shell?
Secondly, I have quite a number of useful scripts available in the Nautilus scripts folder these scripts are available to me via the Nautilus script context menu where I can pass file-names to them for processing by clicking on files and selecting the particular script, to do serious work, will this process be available in Unity?
Lastly, another useful thing is the Templates folder, document files or scripts placed here will be available in the right click "Create Document" menu item, when the document of interest is clicked a copy is created in area that you right clicked, as simple as this is it is a very useful thing, will a Templates folder that facilitates such a thing be available in the Unity shell?
I will be asking the Gnome Shell people about these things too as this concern is applicable to that shell too, being such a dramatic change from the old Gnome interface.
These will still be available in Nautilus file manager unless the nautilus developers decide otherwise. They probably won't be available in Unity's inbuilt file launcher. However, you can still open Nautilus to manage your files. If nautilus isn't included by default (I assume it will be), you can install it from the Software Centre.
'Where's the line between the dash and the file browser?' is a similar question.
Nautilus is expected to be default file manager in Gnome Desktop. It won't be completely replaced by Gnome Shell, only some parts of it. I hope the same applies to Unity.
Nautilus will remain the default file manager in Ubuntu 11.04 - Unity doesn't change that. Although there is some long-term idea that Unity will eventually be able to do data management better than managing files & folders with Nautilus, the Places work isn't there yet. Nautilus will ship prominently (it will be on the Unity launcher by default) until a time arrives where the Unity Places work better for everything.