Does transcoding (for example GSM<>PCMU) negatively affect the sound quality, even when the CPU seems to be ok with it?
If yes, does recording 2 legs using the same codec (say G729) to a different sound format (say mp3) have the same (negative) effect?
Any conversion between lossy codecs will cause a drop in sound quality.
That'll be amplified if you use >2 codecs such as when you receive a GSM call, record in MP3 and playback to a G729 call.
Not only are you throwing away stuff, but they're not throwing away the same thing so the result'll sound worse than either codec on its own. That said some throw away more than others and G.711 (PCMU) shouldn't be too bad.
Using something that doesn't throw away anything for the recording will minimise that. WAV files are good for that and also use barely any CPU, but will increase storage space.
When you use G729 on both legs (using mod_com_g729), it is even possible to record to mp3?
If you're using mod_com_g729 you can transcode so providing you have a license available, yes.
Everything gets decoded to the raw audio by the core then encodes to the desired codec (to send to the other leg, recording, etc). So all combinations are possible providing you can transcode the codec.
-Steve