Let me get straight to your questions.
First we do have any direct experience with the nopCommerce system.
The answers to the second and third questions lie in the fact that the major difference between RadScriptManager and ToolkitScriptManager is that the former combines all script files whereas the latter - only those of the Toolkit components. So, since you can have only one ScriptManager on a page, the better option is to use RSM instead of TSM as in this way the scripts of our controls will also be combined. This will also eliminate the need of removing the Toolkit components from the nopCommerce system.
I hope this information helps. Please let me know if you have additional questions.
All the best,
the Telerik team