Don't skip the formalities, but after a "Good Morning!", just pause for half a second or so, then continue with your agenda.
What "Good Morning" means
When you say "Good Morning", it grabs your supervisor's attention, and under normal circumstances he will just intuitively wait for your concerns at hand (in this case, your task status update). Thus, to him, a greeting is just a formality, and is secondary to the purpose of your visit.
I have worked for a couple of companies during my Industrial Attachments during college, and I am also faced with similar situations like yours.
Me: Good Afternoon!
After a few moments,
Supervisor: Yes what do you want?
From that point on I realised that since the formalities were just a way of starting to bring up your agenda, I changed my salutations to be as follows:
Good afternoon! (pause for half a second) This is an update on my progress on the project, ...
This takes away the awkward silence that ensues when you wait for him to reply you. Don't skip the formalities though, otherwise it would feel like as if you are barging into his office.
Why superiors don't reply to greetings
They often have a busy schedule / several tasks at hand and may be in the middle of a task when you arrive at their office. Therefore, the primary purpose of your salutation is to make your presence known, and not so much of expecting a reply. If you start to talk about your agenda and he stops you by saying,
Give me a moment as I finish this up...
Then the silence is no longer awkward and you can continue to speak after he's done.
P.S. not sure if awkward is the right word to use here, but it does carry the meaning.