It will be worse than that. Nukes? Try bio-weapons too.Unless the war breaks out very early, think before 1950, both sides will have superbombs and won't be afraid to use them. If the war takes place in the 1960s, both sides will have enough ICBMs for this thing to go in a horrible direction. Think Japan getting blasted back to the Stone Age, but the West Coast of the US being obliterated.
Ishii and his team will have many more years to perfect their trade as long as there exists few or no rivals for Japan in the Pacific. IOTL the USSR had plans to distribute weaponized smallpox, among other things, after a nuclear exchange. If Japan's working in a similar mentality then the after-effects of a Japanese-US nuclear war would be worsened considerably.
This makes me wonder if some of the more ideologically inclined but not insurgent minded Southerners would migrate to like South Africa or something. Maybe ITTL instead of "Argentina is Nazi land" we'd be getting "South Africa is Freedomite land".The popularization of air conditioning and cheap living costs will probably also result in Yankee migration south like in OTL. By 2020, I wouldn't be surprised if most of Dixie's population is composed of immigrants and transplanted Yankees and their descendants.
Japan would also probably take in some scientists.