Some time ago I've discovered that MAMEWAH after scan does not see games that are chd only for example Taito FX games. I have to put entries for this games manually.
Also after scan MAMEWAH skips bioses but still adds entries for custom chips like NMK004, QSound. Again, I have to remove those manually.
I didn't know about this but I guess if there are no 'roms' as such then I guess that would happen. The bios romsets are skipped as you say...I am not sure how the custom chips you speak of are flagged in the xml output?
You could create an xml or dat file and set your list generation method to use this (and not check for roms). You would need to make the file only contain games you have / want to show up though.
Any plans for MAMEWAH update? I would really like to see option for rotated layout/display 
I'm finding myself too busy to spend much time on it so no plans for a new 'official' release as such. HOWEVER, I have made myself a slightly modified version for vertical monitors. If you want me to sort you out with a copy, please let me know.