After some further testing, I still don't understand why it doesn't work with GB Pocket. I have tried some extra 1000 uF on all four electrolytic capacitors, but without any effect, except that noise gets worse. 100 uF added to what seems to be the CPU power supply cap (C12) didn't change anything either.
I have isolated and grabbed the signal from the CPU, but it's just as bad as post-amp. A low-pass with 47 nF to ground pre-amp reduces the high frequency, but of course also filters the audio signal. So it's not the amp, the noise seems to come right out of the CPU.
I still still hope that I just have to put an extra capacitor somewhere to get the same noise-filter as on GB Color.
Could it have to do with the boost converter? If you know why GB Pocket is different, please let me know. Thank you.