I think it´s more a chill pill for a) the socialists in her government and b) the people who oppose Gitmo overwhelmingly, and have been eagerly looking on how Merkel supported Bush 2002/2003. Of course she will address that topic seriously, but she won´t risk that her visit becomes a failure because of that.
Do you think were at war with Al Qaeda? If you do, can you name another war where POWs let alone enemy-combatants were "judged" while the war was still going on?