Hand gestures do indeed have a purpose in the real world. The Navy in particular relies on them during flight deck ops because the sheer noise and ops tempo make electronic intercom unfeasible. USAF uses them too albeit for differing reasons. When you're in Last Chance you use hands to talk to the ground folks lookin' you over. For transient jets at airfields unaccustomed to handling something like a fighter or lack the compatible GSE gear, the pilot will brief the ground support people about what gestures mean what.
When airborne, sometimes it's just easier to flip a hand signal than to key up a radio. If you're having radio problems, hand signals are used to relay your status. The catch is the guy/gal you're signalling has to be close enough to see it. Not Thunderbird close, but inside of 100 feet or so (pilots have pretty good eyesight

). And even with all the fancy shmancy comm gear nowadays, sometimes it's more secure to use hand gestures with your wingman for comm sec purposes.