Filtering top level categories by manufacturer doesn't work with SEO suffix disabled. This is because product model is initialized during routing before manufacturer ID is available:
https://dev.virtuemart.net/projects/virtuemart/repository/virtuemart/revisions/11315/entry/branches/com_virtuemart.4.4/components/com_virtuemart/router.php#L1627.
The model then sets empty/false value for manufacturer ID in populateState() method:
https://dev.virtuemart.net/projects/virtuemart/repository/virtuemart/revisions/11315/entry/branches/com_virtuemart.4.4/administrator/components/com_virtuemart/models/product.php#L196.
Models generally should not be reading input variables. Else the variables need to be reset to actual values. Or they can be passed explicitly, e.g. to sortSearchListQuery() here
https://dev.virtuemart.net/projects/virtuemart/repository/virtuemart/revisions/11315/entry/branches/com_virtuemart.4.4/components/com_virtuemart/views/category/view.html.php#L303
Using VM 4.8.2.11343.