No, he is not at all joking.
You should have gone for the head
Let’s not forget that Avengers: Infinity War is Thanos’s movie. It opens with Thanos and it ends with him.
1. We see his home planet Titan, that was ravaged by overpopulation.
2. We see his genuine love for Gamora (after all, he wouldn’t have gotten hold of the soul stone unless his love was true).
3. We see him show respect for his enemies (he tells Tony Stark that he has his respect).
4. We also see him walk away from killing his opponents on many occasions.
Thanos is a very complex villain. In my opinion the best villain by far in MCU, I really like his story arc. He is the dude to deal with, Or as Drax says to Peter Quill, “You’re a dude, he’s a man.”
As a villain, Thanos is unquestionably the definition of what constitutes a great foe. Brilliantly complex, driven, capable of holding his own against the heroes, and has a world-view, although evil, nonetheless, true.
It’s easy to sympathize with him. Despite his evil intentions. For a large purple guy, he’s very believable, maybe even noble.
So, when it’s close to the end, and Thor flings Stormbreaker into the chest of Thanos, he says, “You should have gone for the head,” you can see it in his eyes, he is once again showing respect for his enemy, maybe even making a small joke, by telling Thor that a headshot (or a shot that would have severed his arm from the Infinity Gauntlet) would have prevented him from what he does next… (snap his fingers and kill half of the population of the universe).
We see how he feels about lying through his scene with Gamora when he shows her that he knows she found the location of the Soul Gem. He’s wounded that she would lie to him.
He doesn’t esteem lies.
It’s indicated over and over again that Thanos says what he means.