I ran my own test. I added several notes and highlights to a non-DRM ebook on my Touch and copied it over to my PC via USB. I then opened it in Sigil. Alas, I do not see the notes in Sigil. I also opened the ebook in Nook for PC and the notes and highlights are NOT there. I also noticed that the date on the epub file had not changed since the first time I got it from Gutenberg many months ago.
So, I have to conclude that notes and highlights are NOT stored inside the epub file. I looked around in the Touch's directories while it was tethered to the PC and couldn't find any added files that might contain the notes for a particular book or any book.
It seems that notes and highlights must be stored somewhere in the Touch's memory, which of course is very bad news. I suppose you could search this forum for more info about this topic. You could also look in the Calibre and Sigil forums in Mobilread. Too bad about this.
Hopefully I'm wrong...