Update: so after playing around for serveral hours I found a solution for me. I tried in Windows 7 and XP, both with the same reasults. It seems to me that my SH3 cannot handle all the additional data. When I reduce IABL's Merchant Mod by half and install it in addition to Wilhelmshaven Mod it works. I tried increasing the number of addon ships slowly, and soon came to the point where the game simply went to a CTD no matter which ships I took
Nevertheless it works now and I'm reasonably pleased with the result. After all I have now almost five times as many ships as in stock SH3.