Thank you for your answer, and apologize for my English!
When I mentioned to add the heavy flak to the conning tower type #1, I was not aiming to replace the light flak with the heavy flak.
In game, if you select a type IXB when it is first available (1940), you get the conning tower #1 with a light flak (on the tower) AND a 37 mm heavy flak (on the bridge).
If you look on upgrade menu, under the conning tower #1, you see:
1 gun
1 light flak
1 heavy flak.
The problem is that if you upgrade from the sub type IXB to a type IXC (and later IXD2), you still have the option to use the conning tower #1 (as for the IXB), but only with the light flak gun (no more the 37 mm heavy flak on the bridge).
As I said, I have seen pictures of IX boats with a single light flak on the conning tower, and an heavy flak on the bridge.
Look at the following screenshot I took some time ago.
http://img124.imageshack.us/img124/892/12616is.jpg
The sub is a IXD2 with the conning tower model 1.
You can see that, on the bridge, the area (red marked) where the heavy flak gun is supposed to be is clearly visible.