Most of my opinions regarding codices remain unchanged with the recent changes to version N3, but there are some additions worth elaborating on. There is now an additional merit to the gold codex - the ability to produce more glamour from just pillow books has a very useful mid-lategame utility now, as you can trade 100 glamour for a catgirl warrior. These come equipped with random armaments and a wardrobe including an armor for ground combat, a space suit and a flight suit. The last one enhances a catgirl's stats and further solidifies them as the supreme fighter pilots.
With the changes to the pirates vs ninja war, it's worth noting that some codex craft fare better than others. Having access to craft faster than 2200 knots, or even faster than 2450 knots in order to outrun ninja jetfighters and jetbikes respectively. Since their hunter-killer detection radius is so big, you may want an option to lure them away if they're getting too close to your transports, or even run if your gunnery's not up to par. The green codex is at a disadvantage here as they are once again slow and if caught by ninjas their craft must fight their way out or die. No codex has a hidden advantage in the earlier stages of the ninja war - ninjas will not send out seekers and ground assaults to your hideouts if you are not crowned, which for a codexless player does not happen until the end of the primal hunt arc.