I have been trying to create a daemon using
/etc/init.d/myservice and it will call a shell script that contains
nohup within the script line.
Will it affect it if I could do
service stop later?
Nohup just blocks SIGHUP. The rc script to start or stop your daemon could use any signals at all to shut down your process.
This link has a good overview of the things a daemon process needs to do on startup, for example closing