This sounds like it doesn't have very much lore and reason to it... But also, Shadow Bonnie is the game series' most mysterious character, and also my favorite character. So lets get the show on the road!
Lets start with what I think he represents...
There was a comment on a Dawko video of FNaF AR about Nightmare representing the Crying Child's fear and relationship with his dad, William Afton. Basically, they compared Springtrap's AR voicelines and UCN Nightmare's voicelines. They both say pretty much the same things: "You will not be spared, you will not be saved" and other voicelines but in a different voice. This is a very well done theory by them, but we aren't done here yet.
If Nightmare, since in the game code he is called Shadow Freddy (at least that's what's I've heard) represents the Crying Child's relationship with William, then Shadow Bonnie MUST represent someone or their relationship with another someone... RIGHT?
Ok, next we have some pretty deep lore.
Shadow Freddy isn't a hallucination, but Shadow Bonnie and Nightmare ARE. Shadow Freddy in FNaF 2 is a suit that REALLY HAS WIRES AND INSIDES TO IT! And in FNaF 3, William literally uses it to lure animatronics into a room that is pretty much invisible to them, using the Shadow Freddy suit thingy TO TAKE THEM APART.
And this means... Shadow Freddy is a physical actual existing thing in the FNaF universe.
And with Nightmare and the other nightmares not existing... "WAIT WHAT?" I bet you are asking right now. I will explain a little. The nightmares really ARE nightmares. They are fake. The only reason it kills you to not guard yourself is because of lots of panicking and heart attacks. That's why the Crying Child really dies to these fake things.
With nightmares not existing, and so doesn't Shadow Bonnie, then he HAS TO HAVE TO REPRESENT SOMETHING, THERE IS NO WAY HE DOESNT!
Since the Nightmare was the Crying Child and his dad thing... Why not Michael and his dad? I mean, CC and Michael are both sons of him, both boys, and they are apart of the Afton Family. And as I know, and what you most likely don't know, is Michael is the guard in FNaF 1, 2, 3, 5, and 6. All except FNaF 4 and the upcoming Security Breach (so I don't know he will ever be in this game, but I am much sure the guard is a girl bruh). Another thing I know is that he used fake names throughout his night guard journey.
Michael Schmidt, Jeremy Fitzgerald, and the guys in the other games are all just names he made up for some reason, maybe to hide his identity if he breaks any laws that have something to do with the Fazbear franchise?
Also, we might as well count the dad part in, right?
Another thing is, Shadow Bonnie just enters the middle of nowhere, out of nowhere, and just straight up gives a child a delicious cake. Relationships are confusing as HECK.
So it's settled, the identity of Shadow Bonnie is... The representation of Michael and his relationship with his dad, or his terrible never-ending life of living forever as a disgusting purple person.
Even I don't like the sound of this theory being true.
And here is what they theory was originally gonna go like: It was gonna be him representing the William before the spring lock thing, when he just went around killing kids for no reason... LIKE A NORMAL PERSON!
By jove... Twas a theory, thy game theory!!!
