Frame skip 0 works for a lot of games, but it's still not officially supported. Notably, frame skip 0 can make the emulator itself crash outright, due to a bandwidth limit in the DS-to-DSTwo link in the cartridge pins, or a nested VBlank interrupt, or something like that. Frame skip 0 is there for the games for which it works well, and you should not be using it for all games.
ichfly's GBA emulator is odd; it emulates backgrounds larger than on a GBA, and it has enough information to show 256x192 pixels of overworld maps in some games. But in others, it displays garbage in the remaining columns and rows (from 240x160 into 256x192, so 16 columns and 32 rows). The sound is very poor in some games. And you get to select one of 9 emulation backends, I believe. Maybe the topmost one, chosen by default, is suitable for more games than the others, but I haven't tried all of them.
I don't know what the DSTwo's CPU is set at when it's running code on the DS. Presumably it would enter various
idle states, waiting for the DS to
ask the DSTwo for data from its microSD card, so the CPU's clock would be largely irrelevant for the DSTwo's overall power consumption.