An odex file has the same name as the apk file it is associated with. For example, framework-res.apk has an associated framework-res.odex file on your device.
Deodexing may be better stated as re-dexing since the process re-dexes the odex information then stores it in the original apk. When this process concludes, your phone only has 1 file associated with the app. In my example above, it's framework-res.apk.
Why is this good? Theme modifications affect apk files such as framework-res.apk. However, if you aren't deodexed, then when you attempt to load up a new de-odexed framework-res.apk supplied by a theme artist, your DX will continue to use the old framework-res.odex. This can cause confusing and unpredictable results.
rooted/deodexed 4.1.1 (JRO03O)
Franco Dailies: r295