Hi Nicolas, OK, that seems to be the issue. However, that means this is an issue for any Hikashop site, right? ven of you are not aware, many sites will have product URLs with the /component/hikashop/ format sitting somewhere. Speaking as a non-programmer, I would expect any component that sets canonical URLs to remove the Joomla-generated canonical. As an example, the Canonical plugin by Styleware corrects known issues in Joomla-canonicals by removing the one from Joomla and generating it's own.
Since Joomla cannot "know" that a component generates it's own canonicals, you cannot blame it for generating one, right? So I guess that this is something that should be looked at by Hikashop?
On the practical side, I will probably reroute the incorrect URLs using a 301-redirect (either in Joomla, or using SH404SEF). Since my shop does not have many products, that is no problem.