try this short line:
awk '$2=$2" "sprintf("%.3f",$2)' file
with your example data:
kent$ echo "string 0.998663 string string string
string 0.998592 string string string
string 0.999096 string string string"|awk '$2=$2" "sprintf("%.3f",$2)'
string 0.998663 0.999 string string string
string 0.998592 0.999 string string string
string 0.999096 0.999 string string string