Hi,
Finally I decided to make a clean install of hikashop on my localhost. Deleted all hikashop tables in phpmyadmin, uninstalled everything from Joomla 2.5.8 backend and also deleted some language files left behind after uninstall. I reinstalled hikashop, everything is imported now fine. The only thing is, I created taxation categories after I made the import, checked the tax codes, and I wanted to reimport my data only using :
"product_code";"product_tax_id"
"000000000001";"1"
"000000000002";"2"
to update the tax categories of them, but it did not update, in the product editing pane in the backend still not calculated the price with tax value, and no tax category assigned to the products.
The strange is that, if I export the products, default currency id and tax_category is exported fine as it should appear for the products. 
How the products are deleted from the database, because I noticed that when I delete some products from the hika admin the products are still in the database ( not a problem, specially when someone mistakenly deletes something) but how can they be properly deleted not to affect the other parts of the shop, just to make a complete product cleanup?
Thanks