Hi,
HikaShop has no code to add empty spaces.
Change the type of the field to "text area" instead of "wysiwyg" and you shouldn't have that behavior, which would confirm that the problem isn't in HikaShop.
Also, I tried to use the "wysiwyg" type with the none editor for a custom product field and I'm not able to reproduce the issue on my test websites. I can edit the variants as much as I want and I don't get extra spaces. This further indicates that the problem is not in HikaShop, but in a plugin being triggered and adding these for some reason (bug ?)
When you use the "wysiwyg" type, you're using an editor from the joomla editor plugins. Even if you select "none" as editor, you're using the "none" editor plugin, which is still an editor plugin. And when you use an editor plugin, all the editors-xtd plugins (plugins that add functions to all the editors) are also triggered, as well as the system plugins.
So if you want to get to the bottom of that issue, you'll have to disabling the plugins one by one on your website and test each time in order to identify which one is doing that.