Why is it an accusative noun? Is it because it can be "I give you a welcome" or something like that?
Certainly! In Esperanto you should use Accusative with greetings and wishes because you are giving them to someone
It appears to be mostly a greeting, so far. Nedankinde is the word that is closest to "You're welcome" that I've learned so far. It literally means "No thanks necessary"
Kvankam, mi estas komencanto. :P