Mohamed,
Here are screenshots with brief description for one product "Irregular Cut Bib Collared Dress" size "6Y".
SHIPPING LIST:
SHIPPING RECORD THAT IS USED IN THESE EXAMPLES:
MAIN PRODUCT RECORD:
VARIANT RECORD WITHOUT WAREHOUSE SETTING:
CHECKOUT WITHOUT WAREHOUSE SETTING:
VARIANT RECORD WITH WAREHOUSE SETTING:
CHECKOUT WITH WAREHOUSE SETTING:
What this shows is that if you are using 'warehouse' settings for different shipping methods and the variant record does not have the warehouse setting, it will not find a shipping charge even though the 'warehouse' is indicated in the main product record. If you set the 'warehouse' setting in the variant record, it charges shipping.
My point is that if a variant does not have a setting for any field in the variant record that has the same setting in the main product record, then HikaShop should see what the 'default' setting is in the main product record and use that to make it's calculations. Now my gut tells me that most of these are probably being done but, from testing, it is not working for 'Warehouse'.
I hope this gives you an indication of what is happening and you can fix this problem.