Hi,
Can you check that you don't have the SEF system plugin enabled in the Joomla plugins manager ?
You say you don't have it activated, but it often comes from it.
The canonical URL system allows you to avoid duplicate content on your website. Do you have pages outside HikaShop which can be accessed via different URLs ?
If you do, then, instead of using a SEF plugin which adds a canonical URLs to all the pages, use one where you can decide for which component the canonical URLs would be added, and thus exclude HikaShop's pages.
If you don't, then you can just lead that plugin turned off.
Having several canonical URL tags on your pages is not valid. And what the SEF plugin does, of using the current URL as canonical URL won't help you avoid duplicate content SEF issues. So removing the HikaShop canonical URL, or using the canonical URL given by the SEF plugin won't help you.