Hi nicolas,
I have been using an SEF component named AceSEF for over a year now. They have an extension to their base component for HikaShop. Since your latest upgrade I have pointed out a few changes that they needed to make to their extension. During this discussion with them they have pointed out that certain URL's created by HikaShop do not include itemID's and are the cause of incorrectly created SEF URL's.
The developers there recommended I bring these to your attention. I am not sure if you want to spend time addressing them but if you do I can work with you to correct them and give you more specific examples.
Mainly it concerns URLs related to HikaShop Addresses, categories, account details, and logging in and out.
Let me know if you are interested in following up.