If you want remove the first level, then you have of course to use alias in main menu and real category link in a hidden menu.
But this is only the case for the first level of categories.
Another solutions, is to create an override of the breadcrumb module, or create your own breadcrumb module. I have already code similar request for my customer(eg if a breadcrumb item have no link this need to be removed for google snippets since last year)
The logic is to verify if you have in request option=com_virtuemart. If it's the case, then you write your own breadcrumb links.