Yes if you leave it on a bike for a thief yes it will disappear. Stuff that you can take off easily like an Ortlieb pannier is ideal rather than more complicated stuff that you might tend to leave on the bike . Obviously though if you are leaving something out something less nice or that looks less appealing is useful but I wouldn't really leave any bags on my bike if locking up for any appreciable amount of time.

I would get one of those pannier backpacks that Ortlieb or Arkel make or just use a regular backpack and a milk crate which usually happen to be behind the university dining hall if you want a little risk in life or you can probably get a facsimile at Ikea called the Schmoofung or Düngöl (totally making that up) or find people locally selling them.