Uncle Henrik really is happy that Annemarie has gotten there. And he is happy that the dogs smelled the handkerchief, but he does not really care that he actuall has gotten the package. I think that he is not just being polite, but he is not really thanking her for the package. Instead, he is thanking her for what she has done in bringing it.
We are told that the handkerchief was important because it ruined the dogs' sense of smell. Now the dogs will not be able to sniff out the people that are smuggled on to the boats. This means it was very important for the dogs to smell the handkerchief, but not really important for it to get to Henrik afterwards.