As Nuronv states, in Android 4.0 Ice Cream Sandwich, the sub folders are synchronized. However, I have found in my case that only a partial list of sub-folders are synchronized.
I have server-side rules set up to sort all of my mail into very specific folders and the client is configured to save replies in the same folder with the email. This allows me to maintain collections of emails and conversations with a specific client, vendor, or project. I literally have hundreds of folders and sub-folders.
In my first experience synchronizing, it only caught 3 sub-folders on the 2nd level (I have about 8), and in each of those folders, it found 3 in one folder that I have over 40, and 8 in another folder where I have about 15. It does not seem aparent why this is happening.
I will take Nuronv's second suggestion and go check out Moxier or Touchdown.