From pictures online, it appears that the IJN carrier aircraft used several different colours and cam schemes over the course of the war.
Notably I'm looking for the colour on the following planes; Mitsubishi A6M2, Nakajima B5N2, Nakajima E8N2, Aichi D3A1, Aichi D3A1A, Yokosuka D4Y1. Specifically the colour that the planes being carried by Kido Butai in June 1942 would have been.
Thanks!
For the most part, the planes at Midway were in the same color scheme that the were in at Pearl Harbor.
The A6M2s were a not-quite-white with a black engine cowling. Unfortunately, the photos in my various books suffer from a serious problem: color reproduction (if they're in color at all). So, depending on the book, the "Zero White" is a cream, or has a faint pale blue tint to it, or is really a pale gray. The cream seems to be the most likely.
The D3As were on the whole painted the same as the Zero. I've never heard of a "D3A1A", and can't find any reference to it during the battle of Midway, so I can't help you there.
The B5Ns were more or less a forest green with black cowling. Their underside was, essentially, Zero White.
All planes would have been showing a bit of wear after long months at sea and in combat.
It's funny, but I don't think I've ever seen a color scheme for the two D4Y1-Cs at the Battle of Midway. Certainly most, if not all, later marques were green with white undersides, but I'm not willing to go so far as to say the prototypes were as well.