For some reason the default virtualmin install does not have index.shtml in the Directoryindex directive. To enable it, one must edit the directive:

Virtualmin > Services > Configure Website > Edit Directives 

Find the following line:

DirectoryIndex index.html index.htm index.php index.php4 index.php5

Add index.shml at the end  of the line:

DirectoryIndex index.html index.htm index.php index.php4 index.php5 index.shtml

Click “Save” then “Apply Changes” (on the top right hand side of the “Virtual Server Options” page). Checking your virtual website will show the index.shtml page.

To make it a default configuration

In order to enable  this for all further virtual websites:

Continue reading index.shtml and #include virtual in Virtualmin