Ah, the real answer: when you use a pipeline, you force the creation of a subshell. This will always cause you to get an increased number:
#!/bin/bash
echo "subshell:"
np=$(pidof -x foo.bash | wc -w)
echo "$np processes" # two processes
echo "no subshell:"
np=$(pidof -x foo.bash)
np=$(echo $np | wc -w)
echo "$np processes" # one process
I'm honestly not sure what the shortest way is to do what you really want to. You could avoid it all by creating a lockfile - otherwise you probably have to trace back via ppid to all the top-level processes and count them.