You are most likely familiar with the TCA control setting enablecolumns, as well as the flags hidden and delete, that change the way records display in the TYPO3 backend. Extbase follows the same rules.
Some nice improvements found their way in the Repository functions since TYPO3 version 6.0 to help you on the way to use those fields and limitations in your Extbase Extension.
We updated our Wiki page describing the TYPO3 Query Settings accordingly, please find in the Forge Project page.