Hi,
Go in the Variants tab of the product edition page and delete the variants that you don't want. That way, if a characteristic value is not needed for the other characteristics of the product, the value won't display.
If however you need to value for other variants (so if the other colors are used for other variants that you didn't delete), they will still display but the add to cart button will be removed when you select the inexistant combination.
In such case, there is no easy solution to dynamically modify the selections on the fly. You can either, keep it like this, or customize the code of HikaShop to have dynamic selection (hard to do, even for a developer), or change the display mode to "list" or table" for the characteristics in the HikaShop configuration so that you can only see the existing variants.