The short answer is yes. Since the SQL part is not evaluated by QlikView other than passed on to the driver, should MSAccess is able to interpret the union query QlikView will load all rows properly. You can easily check that using the Select.. button in the Edit Script window. You can see there all available tables and views (queries) and fields in each of them.
Another option, as Sunil suggests above is doing the UNION in QlikView, based on two separate SQL statements.
Hope that helps.