Craig,
On the 1937-1948 flathead V-8 ALL of the head bolt holes go into the water jacket, so what you experienced is normal. A non-hardening sealer(I like Permatex #2) on the bolt heads will prevent leaks. If yours is not leaking, I suggest you leave it as is, and do not remove it again just to apply thread sealer.
Bob Schuman,CLC#254