Is there a way to automate the creation of embedded indexes in hundreds of pdf files?

You can use an Action in Acrobat Pro to do it. Go to Tools - Action Wizard and create a new Action.

Add to it a Save command (from the Save & Export sub-menu) and then click on Specify Settings underneath it.

In the dialog that opens select Embed Index:

Now simply run the Action on your files. You might have to do it in batches, though, as Acrobat is not very efficient and displays each file before processing it.