Sorry, I wanted to reply much earlier, but then I had a little computer crash shortly before my answer was ready....
To be honest, I wonder if this is really worth debating, because we shall probably never know, for certain, what was going on on Leonardo's mind and what was influencing him.
Sure, but we can tell the people with good conscience that Dan Brown's ideas don't match the things that Leonardo and other Renaissance artists have left us (I mean their paintings, sketches, writings, etc.)
As for effeminate-looking young boys, there is no need to try to convince me, personally, because I know that this is so.
I don't really use the term "effeminate" as you may have noticed. But I understand that many people don't want to follow me here.
Like others, he may well have decided that the 'beloved disciple' referred to John,
Who didn't believe that actually? (5 centuries ago)
On the other hand, some people ~ rightly or wrongly ~ have interpreted Leonardo as something of a rebel, who had problems with church dogma.
He was also very clever.
Heretical ideas were flowing around Renaissance Florence.
A number of Renaissance paintings are known to contain symbolism and, perhaps, 'hidden messages'.
If Leonardo had heard some of the heretical stories, and wanted to include them in his paintings, then he would have been intelligent & talented enough to include them, secretly.
He may not have done ~ but it isn't impossible.
Well, if those Dominican monks from Milan, who saw Leonardo's work every day, had like Dan Brown thought that this would be "clearly a woman", then he would have been the opposite of clever
, especially since fighting heresy was traditionally a job of this monastic order. If he wanted to make some kind of heretic joke
then using one of the teenage boys, he liked in a way people from the following century already thought he would, as a model for "the beloved disciple" then this would be more realistic and also much more on the safe side, since those monks or other people surely couldn't identify Salai or other possible models.
Can we see anything that makes us wonder, when we look at Leonardo's 'Last Supper'?
Well, certainly some people can.
They wonder why the boy who is supposed to be sitting in the lap of Jesus is leaning away from him.
See Grrr82CU's answer. It's just about depicting different moments from those lines that describe what happened at the Last Supper.
They wonder why Leonardo left that noticeable 'V' shape between them.
Maybe there is even a 'V' and a 'M' and maybe it stands for 'Vergine Maria' as Jesus has declared some kind of last will at the cross that his mother shall also become the mother of "the beloved disciple". That would make at least more sense that trying to put Mary Magdalene into this picture so obsessively as Dan Brown does.
They wonder why John looks so much like some of Leonardo's female models.
If we compare this figure with others then we'll see that although there's some similarity between this disciple and the heads of Leonardo's women, the resemblance with several figures that are male (especially the naughty "angel incarnate") is bigger.
I cannot tell the difference between Mary Magdalene and St John in these two paintings.
Why should that be?
Why were they painted as twins?
Well, that's these tendency in Renaissance art to give saints this (see my last post) overly youthful look as to say "a beautiful soul lives in a beautuful body" (and that is actually more an old Greek than a Judeo-Christian idea
Maybe, if I could understand that, then I would be better able to understand why Leonaerdo painted his St John looking exactly like another Mary ~ the mother of Jesus.
Not "exactly". As I said before, John resembles much more the young males of Leonardo's paintings and drawings (compare especially the noses and hairlines).