Plot hole: For the shuttle to land at Drax's Amazon hideout he would need a very long runway, something that could easily be detected by satellite.
Plot hole: Near the end of the film Drax tells Bond he had his own shuttle hijacked because he needed it after another shuttle malfunctioned. OK then why didn't Drax just contact whoever he needed to before the Moonraker left on the 747 and have the working shuttle returned to his base before it left. He obviously had the time to get two of his people hidden in the shuttle so a few phone calls would have fixed his problem and the British government would have never had to involve Bond at all.
Plot hole: The British government sends its best agent to the headquarters responsible for a missing shuttle, and Drax immediately wants to kill the man sent to talk to him. Surely Drax would have been smart enough to know if he had Bond killed both the American and British governments would have investigated him, even if he could chalk up Bond's death as an accident.
Plot hole: It would be impossible for Drax to decontaminate the laboratory and remove the equipment in Venice and return it to the room we see in the amount of time given.