When Apps are deployed via MDM, Apple requires an Apple ID and password for the app to be installed. Apps downloaded and installed via Apple Configurator do not require entering an Apple ID and password, however, the iOS device has to be physically connected to the OS X device running Apple Configurator.
With iOS 6, the device caches a users password for 15 minutes. If you install FREE apps in batches via Systems Manager with iOS 6, you will have to enter the password once instead of doing it for every single App.
Paid apps redeemed via VPP redemption codes still require the user to enter a password for EVERY app. Devices running pre-iOS 6 will be required to enter a password for every app regards of whether it is free or paid