With all due respect, I think that there can be different kinds of friendships. For instance,
Aragorn and
Éomer were good friends, and yet they still called each other "Lord". But then Meradioc and
Peregrin just call each other "
Merry" and "Pip". And yet both of these friendships are good.
If you will permit me to draw an example from a book that
Tolkien hated, then in Dune Gurney Halleck is a very close friend to Duke Leto Atreides, despite the fact that Halleck is also his servant. And yet Gurney continues to call Leto "my lord". I haven't come under the impression that this hampers their friendship.
Or, for instance, in 451 Farenhieght Guy Montag is friends with Faber while also respecting him as one much older than himself.
Also, I think that
Sam thought of
Frodo more as of an older brother or a father than as of a friend, and yet this does not neccisarilly hinder their friendship. In fact, I think that it is a crucial part of it, just as it is unimaginable for Gurney and Leto Atreides to be friends without Gurney calling Leto "Lord" and having proper respect for him.