Some categories missing in menu management and not displayed with hierarchy

Im managing a store for a customer who has a very deep category structure, where in the deeper levels there are many categories with the same name but different parent categories. It has become really difficult to manage the menu for this site for two reasons:

1) The Product Categories does not show hierarchy
This can be seen in the following screenshot:
https://www.dropbox.com/s/yyiy7rz2h682mu8/Screenshot%202016-01-12%2017.17.44.png?dl=0
At the left, you can see the Categories box, where the first category shows no child categories, but if you check the right window that category does have child categories.

2) The search feature doesn’t help either
Because the many categories with the same name in different contexts (different parent categories), the search feature ends-up useless because we can’t pinpoint which occurrence corresponds to the one we need.

Any tips please?

https://wordpress.org/plugins/woocommerce/