The maximum payload a single pigeon can carry is small, too small in fact to make it worthwhile making.
Using more than one pigeon doubles the chance the pigeon has of going off-course, getting distracted etc.
The bombs were very costly to build
The main problem was, of course, reliability. Despite Skinner's confidence in his behaviourist approach, any number of extraneous variables could halt or misdirect the pigeon. There was so much scope for error that it was practically useless.
Transportation of pigeons would be even costlier as they would need food, ventilation and water, meaning you would have a low carrying capacity. They also did not have the range to hit targets
The government invested in electronics as it was a paradigm shift in terms of technology and therefore more worthwhile, as the potential application was far greater