Disappointingly there doesn't appear to be an interview anywhere that confirms or denies this. The nearest I've seen is an interview with Graham McTavish (Dwalin) which discussed whose idea it was (not why):
Whose idea was to greet Balin with a headbutt?
I’m afraid that was
That’s the only way you have to communicate with people?
Sometimes a handshake just takes way too long!
Did you actually
headbutt Ken Stott when filming the scene at Bag End?
If I did he took
it very well!!
Nevertheless, it appears most unofficial forums have gone with your theory and accepted it is an homage to Viggo Mortensen and his antics in the Lord of the Rings.
I don't normally quote from blogs, as opposed to wiki or film/tv website articles, but this particular blog has a rather nice description of a possible reason for the headbutt:
DWALIN AND BALIN’S HEADBUTT - A neat moment which fits in with the
proud, machismo nature of dwarven culture but also instantly reminds
one of the behind-the-scenes footage from Lord of the Rings where it
became something of a ritual between some of the cast (particularly
Viggo Mortensen, Bernard Hill and Orlando Bloom) to perform a headbutt
with the stunt teams as a mark of honour and respect. There are some
great stories of how Mortensen went around the entire stunt team at
the end of his principal photography for Rings and gave every single
one of them a hit such as this. It became such a talking point and fan
favourite by the time Return of the King was released (with the cast
even doing it at premieres and the like) that it’s difficult to not
imagine Jackson and team being reminded of and inspired by this when
coming up with moments of camaraderie and the like to show the bond
between the dwarves, particularly these brothers.
Other fan sites, in particular the One Ring Forums (an unofficial Tolkien fan club forum) have countless threads discussing the movie, many of which reference the headbutt and acknowledge it as a homage to Viggo, e.g.:
The head-butt greeting Balin and Dwalin share is an homage to Viggo
Mortensen who would greet his friends by saying something endearing
and then slam them in the forehead with his own (talks about in eedvd
commentaries). White light! White light!
So it's certainly possible that Peter Jackson had the idea to bring this silly bit of fun into the Hobbit films, but it appears the idea itself came from Graham McTavish. Whether or not he intended to be a homage, or just a fun thing to do, is unknown.
Alternatively, you might like Empire Online's tongue-in-cheek reasoning behind the headbutt:
In the book, these two are the first to arrive at Bilbo’s house
(Dwalin, then Balin separately). Here, they greet each other with a
head-butt, leading us to instantly assume they’re Glaswegian.