I would like to offer a nop commerce 1.9 theme for free soon and I have a question:
The App_Themes folder is fine for the CSS parts etc, but I have made changes to some of the Master pages, modules etc. How do I bundle these changes into my theme to give to people?
In this case simply include modified files (e.g. master pages) into your package. It would be helpful if you could add readme.txt file to inform other people that you also changed several files outside App_Theme directory
Yes, it might. You will need to check all changes in the changed files. This might also include the CSS files, since a new version of nop might have new or updated items in the CSS file.
When you change code in files, make sure you mark them accordingly, so it is easier to change on a new release.