There's a chance that I'm entirely wrong on this account... But, as I understand the Nobel Prize isn't handed out in the same way as the Emmys or something. It's not decided based on "who deserves it more" or "who's past actions are deserving of recognition" but on "who will make best use of this money". That's why they don't give the prize posthumously.
So when they gave the prize to Al Gore or the organization of which he was part, they didn't do so as a snub to her. They did so because there was still work to be done in his field. Meanwhile, there probably wasn't a whole lot of smuggling still required to get children out of Nazi Germany in 2005.
While it is tragic that she wasn't honored for what she'd done, that's not really what the Nobel Prize is about. Like I said, at least as I understand the prize.