When John is not there, he's there anyway
Dean and Sam's exchange at the gas station at the beginning of the episode can be an insight not just in how they respectively see their hunting life, but as often kids take after their parents, as another example of what - good and bad - they might have learnt from John Winchester.
Dean says: "In a job like this, you can't get close to people, period." He insists that it's easier to cut ties, to not get attached. Thanks to our after-season knowledge, we can certainly assume that his relationship with Cassie maybe what Dean is thinking (Route 666)...but what else may Dean been thinking of?
Or better, what may have instilled in him a sense of being truthful so strong that made him confess to his girlfriend and thus lose her?
I'd say, John Winchester's teachings, about keeping the Family Business a secret, yes, about doing credit card scams, yes, about lying on who you are in order to obtain information and so help people - the end justify the means...all of this, yes, but also, see when Dean says to Sam:
"So, you lie to them?"
The underlying assumption is that you shouldn't lie to your friends. You shouldn't lie to anyone that is really important to you, like your girlfriend, your friends, your family. There's another side to this coin, of course, that the truth might (as in Dean's experience with Cassie) turn against you. As it apparently does with Sam and Becky, too, once she discovers that they have lied to her about Dean being a policeman.
However, what is Dean's experience of John Winchester in regards to friends?
Well. He knows enough, in Devil's Trap, to go to Bobby asking for help, even if John and Bobby's last meeting didn't end so well, Bobby practically ready to shoot John.
I'd would risk saying that John Winchester has taught his sons that even though lying for a good end is justifiable, lying about who you are to those you care about is wrong; that a life of solitude can be compensated, even lived for the good that one does, even when it is not apparent, or there is no clear, direct reward.
John's influence shows up again later in the episode, when Dean and Sam exchange what they know about shapeshifter lore. Dean mentions that: "Every culture in the world has a shapeshifter lore..." - and this make me think of hours passed in the Impala, as John drives and passes on what he knows to his kids, or John checking out books from the library, dumping them on the kitchen table and pointing them to Dean and Sam before leaving for some hunt or another.
In any case, John Winchester has prepared both his sons to deal with the supernatural world, with knowledge and practical resources.
As Dean explicitly let the audience knows a few minutes later:
"One think I've learnt from Dad, doesn't matter what kind of shapeshifter it is, there's one sure way to kill it..."
And Sam finishes the sentence for him: "Silver bullet to the heart."
Another instance of John's presence in the show even when not physically there is the way in which he represents a tie to his sons, and viceversa. Sam asks the shapeshifter posing as Dean a trick question about John, because what John has done, in relation to hunting, only Dean and Sam know. So, John's hunting experience is used as a sort of Litmus test.
Sam: "Didn't Dad once faced a shapeshifter in S. Antonio?"
Sh. : "That was Austin. And it turned out not to be a shapeshifter, was a thought form, a psychic projection, remember?"
As we know, the shapeshifter doesn't convince Sam, due to Dean's left shoulder injured/not being injured anymore.
There is then yet another mention of John Winchester in this episode, and quite a relevant one concerning Dean's relation with his family and with his father. After downloading more of Dean's memories, the shapeshifter tells Sam:
"..I had to stay home. With Dad. You think I didn't have dreams of my own? But Dad needed me...."
"...Hell, I did everything Dad asked me to do, and he ditched me too, no explanation, nothing, just PFFTTT.."
Again, even if the shapeshifter might be accessing the worst of feelings in Dean's mind, it is highly believable that Dean has resentment towards his father - after all, Dean does figuratively jump on John in Salvation when John scolds him for not calling him about Sam's visions, and as John admits, Dean is right. John has been the one parental figure in Dean's life after his mother's death, and one that has had massive influence on him and his development as an adult. At the same time, whereas Dean (and Sam, see Something Wicked) still sees his father as this mythical, infallible hunter, Skin is the episode in which we also get to know what he thinks about John; as twisted as it can be by shapeshifter, the feelings are undoubtedly there.
What John could have known about these events
Two big events could have been in John's range of awareness about Skin.
One is the 6pm newscast by KJFT 'Manhunt in Progress' - where a 'white male, 24 to 30 years of age, armed and dangerous' is exposed at the culprit in the series of local attacks and one murder.
I'm with Dean in saying: "Man, that's not even a good picture". I doubt John might have recognised him from that identikit, and it looks like as if the Winchesters rather use the newspapers as a source of their info instead of the tv newscast - or directly tap in into the police radio-communications, but that might have happened if John were in the area, which we have no idea about.
The second event is the police report about a certain Dean Winchester as the one responsible for Zack's girlfriend's murder, but also being dead. This report would have appeared in a computer search (as it later did in The Benders), but why should John Winchester search for his own sons' police records at this point?
Dean says that he won't have many chances to see his own funeral, but, as a murderer with no known address or traceable next of kin (I'm assuming that Sam kept himself far away), his funeral would probably be a bare necessity and on the state's expenses, with no obituary or any other type of public acknowledgement. I suppose John might get across it by chance when maybe looking for some other information in the same area, eventually...I also assume that he would first discard it as a namesake, then possibly have second thoughts and pick up the phone to check on Dean himself and make sure. Also, Dean's name wasn't revealed in the news broadcast, which may have alerted some local hunter.
John is mostly present in this episode through his sons' words and behaviour, and he is possibly very present to Dean as an example of what kind of life expects Dean himself given the hunting situation: no lying to friends, but that probably means no friends at all (or relationships), or only those (like Bobby) as involved as they are in hunting the Supernatural. John also owes Dean years of silent loyalty and some explanation, because Dean rightly has resentment towards him (and in part Sam) for having left him behind.
Could John have known about Dean's death? I don't think so. Right now, I can figure John Winchester with his nose to the ground, sniffing after the signs of the Demon's passage, oblivious to anything else.
Ideas, comments, opinions?