When green wood is air dried, the first step is to seal the ends. What is the traditional Japanese method of sealing the ends?
Just like in the west, paint or any other locally available material can be used to seal out moisture. Sealing end grain with a torch is another way moisture was sealed, but I don't know if it was only done with finished pieces.
In my opinion, (as someone who lives in a cool, moist climate), sealing the ends isn't really necessary when air drying, provided you have the wood appropriately stacked and in a shady spot. Air drying wood in Japanese carpentry is essentially the same as its done in the west.
In most traditional Japanese structures, paints, vanishes, or other finishes are seldom used, except for some decorative purposes in temples, or occasionally to prevent moisture penetration on, for example, deam ends. Coal tar or creosote may be applied to the base of posts or other footings to resist water damage. One method of finishing sometimes used is scorching with a torch of logs or posts. This seals off the cells of a porous grain and also darkens and highlights the grain pattern.
Source: Japanese Woodworking: A Handbook of Japanese Tool Use & Woodworking Techniques by Hideo Sato (Translation: Koichi Paul Nii)
As far as I know, they did nothing. They air dried which is slow and deliberate. No end seal just proper stacking.