I have just completed my switch from Entourage to Mail and was very concerned about the ability to search .EML file contents outside of Mail. I found a couple of procedures; one is listed here. Both of them apparently will not work in Mavericks. So what to do?
I don't search these old files every day or even every month. So I settled on a technique that requires no hacking, and is very reliable but maybe not as elegant as some would like. I simply use A Better Finder Rename app to add ".TXT" after the ".EML" suffix for batches of files. This converts the files to plain text files as far as Spotlight is concerned. By the time I was done with gathering up and extracting all my .EML files from Entourage I had almost 20,000 files which I divided into folders names as they were in Entourage. After using ABFR app I then forced Spotlight to index them using the Terminal command:
mdimport /Users/[myusername]/Documents/Entourage\ Archive
Substitute your Users folder name and the folder that contains your files. You can also just wait awhile and maybe Spotlight will index the folder right away. Often, it does not do this and you can wait a whole day for it!
Searrching with Spotlight, when I find the file or files I need, then I can delete the ".TXT" suffix, leaving a ".EML" suffix. I can then drag it onto the Mail icon. It will be rendered as a normal email--you can reply to it, forward it, etc. but will not be brought into Mail's database. I have not found a way to drag one of these files into a particular Mail folder.
Usually I just need a bit of information from an old email so I don't bother with the re-conversion. Another option that is easier in some ways is to use the free EasyFind app. It will search file contents but does not rely on Spotlight to do so; nevertheless it is very fast. So you could keep your old Email library on an external drive that is not indexed by Spotlight. EasyFind also allows for Boolean searches and Unix wildcards.