Should the second 你 in 你的身体会告诉你应该做什么 actually be 你你?
"你的身体会告诉你 (Your body will tell you) '你应该做什么' (what should you do)" is indeed grammatically correct. However, consider three '你' in one sentence, especially two '你' back to back just look weird. 

A better writer would rephrase it to make reading easier, for example:  "你的身体会讓你知道 (your body will let you know) 你应该做什么 (what you should do)" 

or 

" '你应该做什么'(topic), 你的身体会告诉你(comment)"

Note:

"有人告诉你你很漂亮" (the first 你 is the object, the second 你 is the subject of the relative clause)

"父親告訴我我出生時的事" (the first 我 is the object, the second 我 is the subject of the relative clause)