Turns out that it is a currency problem, although I thought I had configured it properly (and I did).
Company currency = EUR
User Currency = EUR
Account Currency = EUR
Pricelist Currency = EUR
Storefront Default AND Active currency = EUR
BUT, after digging into a long session of debugging and reviewing the logs at the registered user level, it turns out that the Apex classes in B2BCommerce were returning 0 products because the pricelist currency did not match the user currency.
Actually, when you install the managed package, a new custom field CC_Currency is added to the User object. This field however is not required and does not appear on the user profile and users' layouts. Plus it is not automatically filled.
Therefore the mentioned CC_Currency field will remain empty and will affect the products available to your users.
Apparently, if the field is empty, it is hard coded that 'USD' replaces the empty value, instead of using the related accounts' currency or any other currency for that matter.
I was able to resolve the issue by adding the field to the layout, and updating it to EUR for my users.