Hey Olga and xstore community.
After posting up my own support tiket in woocommerce forum and reading up woocommerce forums I tracked down the problem.
Woocommerce has bugs.
The issue is the data in the lookup table( this became more apparent when I forced some terms to show and tried to filter by them and no products would show even when they should the lookup table shows again on the store main query when filtering )
I fixed it by unchecking the Enable table usage in Woo Settings->Products->Advanced
Try also to regenerate the count in Woo > Settings > Products
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