I understand what you're talking about.
You're saying that the module class suffix is not set in the html of modules which are displayed in the component instead of being displayed directly in a position of the template. And that's normal.
The chrome html divs around modules are added by joomla. They are added based on the style attribute in templates :
<jdoc:include type="module" name="test" style="rounded" />
The possible values are rounded, table, horz, xhtml, plus any style defined in the template it self.
In the hikashop component, the style used is "none" which doesn't add any chrome around the modules. And thus, you don't see the module class suffix. That's by the way the same in joomla 1.5 and 1.6
If you want to change that, you can edit the files show and listing of the views product, and the file listing of the view category (via the menu Display->Views of HikaShop).
Near the bottom of those files you will find the line:
echo JModuleHelper::renderModule($module);
which you can replace with:
echo JModuleHelper::renderModule($module,array('style'=>'xhtml'));
for example to use the style xhtml of your template for the chrome of the modules displayed there. Then, joomla will automatically add the chrome, with the class suffix in it.