I would also shut down IBM Domino Diagnostics and IBM License Metric Tool in the shutdown batch file. These run as Windows services, and can be shut down with net stop >service name> as the Domino server task itself can be.
Another approach to the shutdown delay is to use program documents to stop Domino tasks on the server based on the schedule followed for Windows Updates. For example, if Windows Updates are installed at 1 am on Sundays, then schedule the shutdown of tasks such AMgr, Router, HTTP, Indexer, Replica, AdminP, etc., through program documents for 12:50 am. With most or all tasks listed in the ServerTasks= line of the server's Notes.INI shut down, you will find that Domino should not take long to shut down completely.