Delete unused master spreads

The alert that you see pops up not when there are no unused master spreads, but when you try to delete a master that's applied to another master or a page/spread. You can't use menuActions for this I don't think because you need to be able to tell whether a master is applied. With menuActions the test is to check whether that alert pops up, but you can't script that.

But it's not too hard to check whether masters are used: create a list of masters applied to the document's pages, another list of masters applied to the document's masters (i.i. a list of masters based on other masters), then remove the masters that don't occur in either list.

(function(){
  
  var pages;
  var masters;
  var i;
  var appliedToPages = {};
  var appliedToMasters = {};
  
  // Get the names of the masters applied to document pages
  pages = app.documents[0].pages.everyItem().getElements();
  for (i = pages.length-1; i >= 0; i--) {
    if (pages.appliedMaster !== null) {

      appliedToPages[pages.appliedMaster.name] = true;

    }
  }

  // Get the names of masters applied to masters (i.e. masters based on other masters)
  masters = app.documents[0].masterSpreads.everyItem().getElements();
  for (i = masters.length-1; i > 0; i--) {
    if (masters.appliedMaster !== null) {

      appliedToMasters[masters.appliedMaster.name] = true;

    }
  }

  // Delete masters that are not applied to any document pages or other masters
  for (i = masters.length-1; i > 0; i--) {
    if (!appliedToPages[masters.name] && !appliedToMasters[masters.name]) {

     // $.writeln (masters.name);

      masters.remove();

    }
  }
}());

Peter