Hi,
This is just a supposition but I don't think that the problem comes from the characteristics/variants themselves.
I think it comes from the customization of the product page layout which is incompatible with the changes made for the 2.6.3 and it breaks the HTML and this results in the characteristics selection area being hidden in the page.
If that's the case, it means that if you temporarily switch to the default Joomla template, you won't have the problem. And in that case, the problem must lie in one of the files of the folder templates/YOUR_TEMPLATE/html/com_hikashop/product/ that you can rename one by one to identify the one with the issue.
If the problem is not there, we would need the link to a page with the issue and a backend access to check the settings since no one else has the problem and we can't reproduce it, so I guess it would require first making a copy of the website to keep your live website working.