I've got good news regarding email notifications in Android 4.4. It seams as subfolder notifications are already possible, only the configuration option to enable the notifications seams to be missing. But using a root file manager (e.g. Root Explorer) the settings can be added manually.
First you have to write down the serverids of the folders you want to be notified. These ids could be found in the sqlite DB of the email app in the mailbox table. (use e.g. SQLite Editor to read the table directly on the phone) The second step would be to encode these numbers to base64. (This is the way Android defines a unique name for the config file) On the following website you can encode the serverids to the base64 string:
http://www.motobit.com/util/base64-decoder-encoder.asp
For e.g. the serverid 17 the base64 string would be
MTc= but in the file you will have to enter only
MTc. The config files are stored in the folder
/data/data/com.android.email/shared_prefs. The eaisiest way to make the preferences for your folders would be to copy the preference file for your inbox and then rename the file. The file is named like this: Folder-YOURACCOUNTNAME-BASE64STRING.xml. Just make a copy of the file and set the base64 string for your folder. (Notifications should already be enabled in the xml file)
When you've done this for all the folders where you want the notifications restart your phone (Android does not seam to register the files without restarting the phone) and short after that you should receive the notifications.