No, the books will not resync unless you sign out of your kobo account on the desktop and then sign back in. I don't sign out, so books do not resync. Starting over from factory reset starts you with zero books on your reader, so syncing everything is necessary. Using a different reader means everything will sync initially.
And yes, if you delete a book from your Touch or from another device or app (including the Kobo desktop), it deletes on any other app or device the next time you perform a sync with that app or device. This includes both the desktop and the HTML5 read.kobobooks.com browser app.