Basil Fawlty is still reeling from having a moose head fall on his own head, so he is mixing his idioms. Notice the "idle hands..." comment just before he said that. The original saying is "a bird in the hand is worth two in the bush" (roughly meaning, "what you have is far more valuable than what exists out there"). Basically, Fawlty has mixed it up and is speaking nonsense as a result.

It is a bit strange in this sentence. However, it comes from the following phrase: A bird in the hand is worth two in the bush. Meaning, having one bird in your hands, presumably to eat, is better than seeing two birds in the bush (which you would have to catch before eating). So I would interpret your sentence in this way: Being hit in the head in that manner, is worse than being hit (in some other less dangerous way) twice.

I would have to know the context to know for sure, but it appears to be an idiom that was improperly used. The idiom says, "a bird in the hand is worth two in the bush". It means that it is better to be satisfied with what you have than to risk losing it to go after more.