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:

In a time, when the cost of maufacturing high quality optics in Germany was on the rise, but was flat in Japan, lens price became the limiting factor for the success of the new Contax. To free the young system of this limit, Carl Zeiss transferred the production of lenses for the Contax system to the country that was buying most of them anyway. In favour of this decision was the fact that Japan has, as well as Germany, a very mature infrastructure regarding the production of photo optics. Also, Carl Zeiss has had a strong presence there already. So Carl Zeiss transferred machinery, know-how, and personnel to Japan and built up a lens production facility that could produce Contax lenses in accordance with Carl Zeiss quality standards.

In recent years the cost advantage of quality optics production in favour of Japan has decreased. Top quality optics made in Japan are no longer really cheaper than those made in Germany. Today, manufacturing costs alone could not justify the move from Oberkochen to Oume. But the strong demand from the Japanese market for Contax lenses would again lead to the de-cision, to manufacture them where most of the customers are anyway.

http://www.dantestella.com/zeiss/japan.html