The Naomi version of nullDC is specifically designed to be used with the arcade machine Naomi, which to put it simply is a dreamcast with some beefier specs, namely memory. As a result many games which were on the dreamcast were ports from the arcade with tweaks to make the games more suitable for home gaming.
Thus, the naomi version of nulldc focuses on the format of these arcade games, rather than the home console versions. Naomi emulation came allot later than dreamcast emulation due to several factors, but IIRC the main one being the encryption used to protect the games. When they were cracked, development was able to begin on emulation.