The Silverplate B-29s did have their turrets removed, save for the twin .50-caliber in the tail turret, but this was becoming par for the course for many B-29s operating in the Pacific. The switch from high-altitude day bombing to low/medium-altitude night bombing for conventional attacks meant that most of the B-29s defensive turrets were no longer necessary. Additionally, the bombing campaign against Japan revealed that that one of the weaknesses of Japanese air defense was its fighters lacked the superchargers to operate at altitude. The performance of interceptors like the Ki-44 or J2M dropped off markedly at altitudes around 25000 feet, so often they could make only one or two attack passes after a considerable struggle by the fighters to get to the altitude of the attacking B-29s. Fuel shortages and maintenance problems also made mass interceptions quite difficult and the Japanese had to husband their air assets which were already wasting away due to attrition and other operational problems.

The training missions for the atomic attacks showed that there was little to fear from Japanese air defense. The 509th carried out attacks on target cities with what were termed pumpkin bombs, large, single bombs that mimicked the planned atomic devices. These attacks were done at high-speed and at high-altitudes. The 509th's pumpkin bomb attacks conducted prior to the nuclear attacks hit the Japanese air defense network at their weakest points. The 509th's raids were small scale, usually a three-plane formation, so the Japanese air defense network did not bother to send up much in the way of interception. The 509th's planes were operating in daylight, but at altitudes of about 30000 feet. This meant that they were a hard target for either interceptors or Japanese flak. All but the heaviest caliber AA guns in the Japanese arsenal could reach these altitudes. Moreover, the Japanese air defense network was stretched too thin and in the process of breaking down completely in the summer of 1945. The 509th's observers did note the presence of some Japanese interceptors during the pumpkin missions, but none of them made attacks on the planes. Only one 509th B-29 received minor damage during these missions, likely from AA.

So American planners were confident that Japanese air defenses were not a major concern by the time of the atomic missions. By August 1945, small detachments of B-29s were flying over Japan in daylight conducting weather and reconnaissance flights on a regular basis. Had a "golden bb" or a mechanical problem caused the Enola Gay to crash, the result might have been a partial detonation or something akin to a dirty bomb. Little Boy's firing switches were quite crude and had the bomb crashed, it is possible that it could have triggered a detonation. There are a lot of variables such as whether or not the bomb's cordite was set on fire, but it was an unsafe design. Little Boy had very few safety features unlike Fat Man or subsequent atomic bombs.

American planners did not completely rule out the possibility that the B-29 could be intercepted. One of the basic proofs of this is the selection of Japan as the intended target of atomic weapons in the first place. Unlike Germany, many American planners believed that if Japan lacked the scientific or technical infrastructure to reverse-engineer a damaged or intact bomb that either failed to detonate or whose mother ship crashed.

Edit: in response to a now deleted comment in this thread on the thousands of Japanese aircraft preparing for a Kamikaze attack:

Japanese command still had thousands of planes ready with kamikaze pilots

This sounds more impressive than it was in reality. While it was true that Japan was husbanding planes for a mass Tokko attack in case of Allied invasion of the home islands, this was less a deliberate strategy than the least-worst option for Japanese airpower. Most of these aircraft were not operationally-ready and many of them were obsolete models. Some of the intended tokko planes were modified trainers or special, one-off monstrosities like the Ki-115, which used an obsolete engine. The shortages of fuel, lubricants, and spare parts as well as ersatz materials such as avgas distilled from pine needles further cut into the potential strength of this force. IJN estimates in the summer of 1945 estimated that around 60% of its intended tokko would be operational to meet an Allied invasion later that year, but this was probably unduly optimistic. Allied military assessments of Japanese airfields and aircraft in the immediate aftermath of the surrender showed that many of these aircraft were in rough shape.

So Japan may have had several thousand planes ready in the latter third of 1945, but this number consisted mostly of aircraft that were ill-suited for frontline operations in 1945. Of these planes, a number of them were non-combat planes impressed for a final blow or obsolete airframes that were available. Even the frontline models like the Ki-84 or N1K2 suffered from shortages of spare parts and decline in material quality. Above all, shortages of fuel hampered Japanese air operations so that a final mass blow was about all the Japanese air forces could do on a macro level. Despite its numbers, Japanese airpower by August 1945 was very much a broken reed.