I figure I should share that I've found in some cases .pbp gives better performance compared to .chd, mainly in games that have voice samples playing during gameplay. That's what I've noticed in Disney's Hercules NTSC, which stutters whenever Phil talks if you use the .chd, and runs smoothly in .pbp. My very rough theory is that it is because .pbp converts audio to a lossy format and .chd to a lossless format, so that .pbp being lossy makes it less taxing on the 3ds.
I've tested this with some other games, but I haven't really found any that plays voice samples while gameplay is going on. Like Castlevania SOTN stops whenever there's talking, and that's the same for most RPGs like Lunar etc.
I wish there was a way to convert to .chd and choose as low quality for the audio as possible.
I tried testing something in the similar vein of this by converting the cd audio of games like Rayman to .ogg, but it seems pcsx_rearmed does not support it and I wasn't able to convert to neither .pbp or .chd afterwards. It would have been nice to see if this worked because it might've been able to get even better framerates, which could help for those couple of games that use redbook audio. Better performance trumps audio quality any day for the 3ds right now, and you won't really be able to tell the difference with the "high-quality" 3DS speakers anyways.