Hi,
If you don't provide the alias, the HikaShop generates it from the product name.
If you have the "Unicode alias" setting activated, then all the characters can be used in the alias and the product name will be used "as is".
If you turn off that setting, the HikaShop will use your Joomla language transliteration system (if any) to convert the characters into romanized characters (there is such system for the Russian language for example, but I'm not sure for greek). And if there isn't a transliteration system, it will just use replace all characters outside the latin alphabet by underscores.
Then, when the canonical URL is generated by HikaShop automatically, it will use the alias of the product. So there shouldn't be a problem with the generated URL, regardless of how you set the "Unicode alias" setting. There would be if you were filling the canonical URL before the alias would be set.
Note also that if you import the products, you can also import their alias in the "product_alias" column.