Recently, I used a Zeiss Makro-Planar T* 2/100 ZE only to find a big "Made in Japan" marking on it. Which of their lenses are made in Germany, and does it matter if it's made there vs. Japan?
The vast majority of Zeiss lenses are indeed made in Japan.
Of currently listed Zeiss (non-cine) camera lenses, only the ZM Distagon 15mm f2.8 is Made in Germany (also in that line, the ZM Planar 85mm f2 was too made in Germany).
Even the super-high end Otus 55mm is Made in Japan (Zeiss confirmed this via their Flickr account in a recent post).
The fact that a lens company who values quality so highly has moved (virtually) all its production of (non-cine) lenses to Japan means you can have confidence that the location of manufacturer is insignificant. If the expensive lenses were made in one location, and the cheaper lenses made elsewhere, that might give you pause. This is not the case.
In terms of the reasoning behind the move, I refer you to Dante Stella's piece from Camera Lens News No. 3:
Currently, it appears that none of the Zeiss lenses are now manufactured in Germany (all Japan). Here is some more info from BH Photo the subject: http://www.bhphotovideo.com/find/newsLetter/Carl-Zeiss.jsp