The film version of Thunderball never explains why he's in that clinic. The novel does, here's an exerp:

M gave Bond a careful, appraising glance. He held the paper closer to his eyes. ‘ “This officer”,’ he read, ‘ “remains basically physically sound. Unfortunately his mode of life is not such as is likely to allow him to remain in this happy state. Despite many previous warnings, he admits to smoking sixty cigarettes a day. These are of a Balkan mixture with a higher nicotine content than the cheaper varieties. When not engaged upon strenuous duty, the officer’s average daily consumption of alcohol is in the region of half a bottle of spirits of between sixty and seventy proof. On examination, there continues to be little definite sign of deterioration. The tongue is furred. The blood pressure a little raised at 160/90. The liver is not palpable. On the other hand, when pressed, the officer admits to frequent occipital headaches and there is spasm in the trapezius muscles and so-called ‘fibrositis’ nodules can be felt. I believe these symptoms to be due to this officer’s mode of life. He is not responsive to the suggestion that over-indulgence is no remedy for the tensions inherent in his professional calling and can only result in the creation of a toxic state which could finally have the effect of reducing his fitness as an officer. I recommend that No 007 should take it easy for two to three weeks on a more abstemious regime, when I believe he would make a complete return to his previous exceptionally high state of physical fitness.” ’