Why is it a bad thing if they now like each other better (not sure if there is real evidence for it but assume it is true for argument's sake)? If American policy is what keeps them apart, which I strongly doubt, then it is a good thing that we butt out and let them integrate as much as they want.
Just because they turn against the US on trade does not mean they are becoming friends. American policy is not what keeps them in part.
In short term they cooperate on tariffs, because America has gone crazy.
On the long term. South Korea and Japan will seek their to ensure their security against China without the US. South Korea is already discussing domestic nuclear weapons. Japan could go nuclear at any time when it wants.
It is not in the abstract a bad thing, and things like this are fairly inevitable under the circumstances. It's probably not a great thing for the US's foreign policy, and particularly trade policy (if you can call the current random flailing a policy) if the cause of it is treating the US as a common adversary, however.
