If you are using the source code version of nopCommerce then it will be best to add the theme and the plugins to your Nop.Web project. Just select them and click "Include in project". This way during the Deploy they will be copied.
p.s: I am talking about the SevenSpikes plugins and the ShopAll theme. It also depends on how your Publish profile is setup i.e to copy all the files in the Nop.Web folder or only the files included in the project.
I've added the directories and files to the project and it looks to be working perfectly now. Thanks again.