Fighter-bombers designed in the 1950s that had bomb bays, like the F-105, Buccanner, and A-5 Vigilante, were originally designed to carry one very large weapon – a nuclear bomb. The drag of such a weapon would be unacceptable, so they put them inside the aircraft. That’s really the only reason they ever had internal weapons bays.
The F-111 was likewise equipped with a bomb bay because of its nuclear role for the USAF, although its bay was more versatile.
None of these aircraft were ever originally intended to carry conventional bombs for tactical strikes inside their bomb bays, and they rarely if ever did. The drag penalty from carrying external stores never really mattered because of the availability of aerial refueling. And radar cross-section wasn’t something anyone cared about back then.
Today, the F-35 is designed to carry a useful load of conventional strike weapons internally, but the reason is purely for radar cross-section. The F-35 is able to carry weapons externally as well, and if it were engaged in one of today’s conflicts like Afghanistan or Mali it would not need to worry about stealth and would carry its bombs outside.
So, in short, the only reason anyone uses weapons bays today is for stealth. Space inside aircraft is otherwise better used for fuel or systems. External carriage is safer and you can carry a whole lot more bombs outside a fighter than inside it. It’s true that a strike fighter would burn less gas if it carried its bombs inside, but it could carry fewer bombs, and it is still cheaper and quicker to hit a tanker than to fly all the way back to base to rearm.
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