I'd assume the issue was rather the game needing the space: the first few CD game generations took 50, 100, 200MB on the disc, so putting the OST in CD format was a nice easter egg. Note that games didn't generally put all sounds as CD tracks, just the actual music.
Once your game starts filling the CD, to say nothing of needing multiple CDs worth of storage, having the OST included is not an option anymore.
It wasn't an easter egg; it was how the games accessed and played the in-game music (and digitized speech when that was a new, exciting thing). There would be one huge data track and then dozens of small audio tracks. If the game did take multiple CDs, then either (a) you installed all the discs but all the audio was on the CD that had to be in the drive for the game to play or (b) each CD had the audio needed for the levels that were on that disc (I think that scenario was more common on PS1 games, but I could be mis-remembering)
Except they never had to do that, even before the MPs, they could always have stored the audio data as regular files on the disk image. Using CDDA just makes things more complicated as you need to reaccess the raw media instead of just reading the data from the filesystem.