Allegro 4.4 is mostly RGB. For proper NES emulation, I would need a YUV color space, but I see only HSV as alternative in Alleg44.

Any chance of using another color space? If yes, how do I put a pixel / its color bits format?

You'll need to write yor own RGV->YUV conversion function. This should help you get started.

Allegro 5 has al_color_yuv_to_rgb and al_color_rgb_to_yuv, so you can use those functions as a reference.