The Vals, true, but the Kates are (barely) big enough to do it. And the Japanese could make their version of the Fritz-X small enough to be carried by Vals, although there wouldn't be much point to it; dive-bombing is already fairly accurate and safer for the attacking aircraft.
You are correct, though; the Bettys and Emilys would be deadly threats with these weapons, especially the HS-293, which can be launched from outside the range of AA. The US would certainly launch a crash program to develop countermeasures, which would probably be in place by mid-to-late 1942. They would also develop their own equivalent weapons, and the Japanese would develop countermeasures as well.
Expect a lot more ship losses on both sides, especially in the first months of the war. Then a continuous arms race in these guided weapons and countermeasures, with the US having the advantage due to its larger resource base.