You've seen the movie? and read the graphic novel?
The answers are in there...
I'm not quite sure what you don't get.
There is a point.
I know the point.
We all know the point.
I suggest you carefully re-read the GN.
Smugness. You must drop it down a notch or two.
I don't think there's any point to Jon's nudity, if there's anything that shows how he loses his humanity, it's certainly not his dangling blue dick.
When you see it in the comic (graphic novel is for hipsters) then it's mostly because of Moore's approach to sexuality in the medium, he has always commented on how people should be less conservative about seeing uncensored sex or genitalia in a comic book.
It shows that he is
losing his humanity.
"You're drifitng out of touch Doc"
Its not literal I don't think.
Its more of a symbolic thing.
It was simply handled better in the comics.
The less he wore, it symbolized the further from humanity he drifted.
It was partly due to veidt's plan all along.
Fighting crime he had the full body suit, yet in 'Nam, he had the one-piece bathing suit looking thing.
Before that actually, the first time we see it is I THINK at the first watchmen meeting.
I wonder if its because he was already asked to do unspeakable things and not feel
Its towards the end of that part where he trades those lines with Blake.
Not long after 'Nam, he downgrades to the speedo, and so on.
The more time he spent as 'Dr.Manhattan' doing all this stuff,
the less he felt like a person.
The less he felt human.
Its simply reflecting in the changes in clothing.
By the time he's down to nothing at all, you know he's but a thread away from just... leaving.
Which was due fully in part to Adrian's plan. He exploited that part of his psych profile.
In the movie, theres no significant progression.
Aside from the protocol at the funeral, he's just speedo - naked.
And sorry about the smugness.