ROMs are typically released in deodexed form because they can be themed and modified fairly easily, whereas theming/modifying an odexed ROM is basically impossible (at best things would crash like crazy). Some people also choose to release their ROMs in odexed versions for people who would prefer the performance gains.
Most of the stock ROMs I've seen are odexed, I assume because the carriers/manufacturers want the performance boost. They also don't have any kind of official theming methods, so they probably don't care if you can't change the colors of your status icons or your system text or whatnot. Plus they have the advantage of knowing what device they want their system to run on, so they can pre-compile the .odex files very easily, I imagine. As an added bonus, it makes it difficult to pull .apk files off of the device and share them with people.
Edit: Since I just realized that I was not very explicit about the difference here - an "odexed" ROM is one where the apps have been precompiled, and thus contain associated .odex files which are external to the .apk files. A "deodexed" ROM is one where data that would be optimized in the .odex files has been more or less merged back into the .apk files (meaning it is not optimized but basically platform agnostic), thus the .apk files are self-contained and there are no .odexfiles. This is usually just done with a deodexing utility, such as
smali/baksmali.