When Thanos arrived at Titan Dr. Strange said "You look more like a Thanos" as if he had seen him for the first time. On the contrary Dr.Strange went ahead in time to see the possible outcomes and he must have seen Thanos in it. Is this a movie plothole?
So, we can now easily check to see if Dr. Strange said anything to Maw when he arrived and the answer is no, he doesn't ask if he's Thanos. Maw makes it clear that it is the children of Thanos that have come to take the stone. This is further clarified in the ship when Strange is held by the surgical needles. Therefore, the answer that he thought Maw was Thanos at any point in time is definitely not correct.
The correct answer could be that he thought the GOTG were somehow Thanos initially, but Strange is a smart guy and none of those people are even remotely Thanos, plus Thanos had already sent Maw after him who proclaimed as mentioned above that the children of Thanos essentially do all his work for him, so he probably thought that they were WITH Thanos. This makes more sense anyway as the general conversation goes when Spidey is caught by Starlord at gunpoint; i.e. "we're the Avengers man!" Therefore, this answer is also likely not correct (although closer to correct than the top answer).
The only answer I can come up with is that Strange is breaking the 4th wall, something that a master of the mystic arts could possibly do, and is referring to Cable. This would be well-within the realm of the self-deprecating humor of Deadpool and acceptable to Marvel, because they would want to maintain that Brolin was always Thanos and not Cable.
I can't find the exact quote, but I believe this is in reference to the initial arrival of Bruce Banner and then Maw. When Bruce first lands on Earth he warns that Thanos is coming, soon after Maw arrives in NYC. I think (and this is the quote that I can't find) that Dr Strange asks if Maw is Thanos. So in the scene, you mention Dr Strange is making a callback to this initial confrontation. This is also supported by Thanos's line after Dr Strange speaks:
Dr. Stephen Strange: Oh yeah. You're much more of a Thanos.
Thanos: I take it that Maw is dead. This day extracts a heavy toll, still he accomplished his mission.
I don't think he was actually surprised by Thanos's appearance; in-universe, it was probably just a bit of banter. You mention that this was an exclamation, but I recall it being said rather calmly.
Of course, the Doylist reason is that it amuses the audience. If he's seen Thanos some 14 million times, even saying that as a joke doesn't make sense. On the other hand, maybe it was necessary to get that one future where they defeat Thanos...