Based on the condition of the body how did Emmett die, and why did it take so long to find the body? Chapter 11

The cause of death was a bullet hole to the head. The body wasn't initially found because it was weighed down before being tossed into the river.

From the text:

Officers said that the body had been weighed down with a cotton gin pulley tied with barbed wire. There was also a bullet hole in his head.