this is not much of a question than a solution to a problem that i couldnt find.
Problem: On category archive made with custom query i could not get /page/2 to work ( always 404 ).
Tried every possible solution in the book, and finally i reverted back to the original query, there i wanted to change posts per page for this query to check if the problem is caused by my custom query. It appears that woocommerce changes posts per page with Apperance > Customize panel and dosn't use the Settings > Reading page. When you set there the number of items per row * number of rows to match your custom query demand all starts to work fine. Too bad that woocommerce had to make it so weird ( i kinda see the point why it is that way, just its very confusing) :D
Anyways i hope this helped someone, i wasted a healthy 2-3 hours on searching for solution. Cheers!