That would depend on how your Access database is set up. If your queries are plain select sub-queries that feed into a bigger query which is then used by Tableau, then Tableau extract refresh should execute the sub-queries as part of the big chain.
But if those queries are of the make-table type, i.e. they create tables that are then used by by other queries, then they will have to be executed manually or via script.
How come when I tried creating a simple select query on Access, saved the file, connected the file to Tableau, it only shows tables and none of the queries are shown?
That is strange. I just tried with sample database that came with Tableau, and I could see both tables and queries.
You may need to contact Tableau Support with this.