Howard makes the effort to hold the stethoscope in his palm first, so it isn't a freezing cold metal instrument against Hiccup's bare skin. He places it there, ding his best to ignore the scars. It's not like he doesn't have some nasty scars of his own either, although nothing that required the extensive grafting Hiccup needed.

"Breathe deep." It's partially so he can hear Hiccup's lungs. It's also partially to try and get Hiccup to relax just a little.