Why do you think Amaral discounted this possibility at the time?
How do you know he did?
Why was Gerry McCann never asked by police if he had been carrying a child around PdL at around 10pm that evening?
How do you know he wasn't?
You seem to assume that the police have revealed every single bit of information they have.
There are things that have come to light since Amaral was removed from the investigation that may, for all we know, have changed his angle of questioning/beliefs about the case.
I will state again that the police (certainly in this country and I have no reason to believe it's different abroad) even though they may pretty much know full well what's happened will not prosecute whilst there is insufficient evidence to do so. As has been pointed out by none other than debunker, absence of evidence is not evidence of absence. Just because the McCanns have not, as yet, been charged with anything does not mean they are innocent of any wrongdoing. Yes, it *might* mean that, but it's not a logical conclusion to continually say, "well why haven't they been charged yet if they dunnit?" The police have plenty of evidence of all sorts which point the finger firmly at a coverup of sorts. What they don't have is admissible evidence that implicates the McCanns to a point whereby a prosecution would be successful.
What is clear to all but you blinkered sorts is that there are all sorts of discrepancies and bits of odd, if not inexplicable, behaviour that leaves a far from clean slate for the McCanns. That you are unable to separate this point of view from that of what you would call a "[ censored word ]" or "[ censored word ]" says more about your mental faculties than it does for anyone that doubts them.