Hi uboatfan,
I don't have much info on the Zwiebel but according to Roessler in Die Sonalanlagen der Deutschen Unetrseeboote was also fitted to the Walter boat U 794. The XXII U 3003 is also mentioned so maybe it was fitted to that boat too. But I'm pretty sure no other IXs or VIICs had them other than U 889.
The hull openings on the stern of U 889. U 889 had a snort at that time so I am guessing it could be the exhaust outlet (when boats were fitted with the snort the exhaust outlet were moved below the waterline). U 858 had a very large outlet in this same location, though it was quite different to the openings on U 889. If this opening was not an diesel exhaust outlet, an alternative would be the outlet for Bold?
The square openings with two smaller sqaures below on the IX in 1940 at Lorient - I always thought these were the exhaust outlets. It is a bit similar to the outlet employed on VIICs in 1942, the exception being the two squares are lower down on the IX. But that is my guess - exhaust outlets.
Cheers,
Dougie