@Curly Haired Assassin
I can have a go at answering your question, mainly because it's quite common and it's been answered many times before, but the answer does tend to lead to another question and some people get upset when that one is answered.
There is almost certainly no placebo effect on babies as the individual being treated.
The placebo effect requires an expectation of result, which a baby would not have.
However, there are numerous other effects that can create a false impression of a placebo effect.
Conditioning is one way that a baby might seem to demonstrate an improvement.
Human touch is often comforting and I've no doubt that Craniosacral therapy can be relaxing.
A baby can, after enjoying a session or two, learn to anticipate such pleasure and as such would be more likely to simulate comfort in and around future sessions.
This effect is magnified by the care-giver and practitioners expectation of result.
This expectation often leads to behavioral changes that babies would be likely to pick up on.
This is of course more likely to occur in a lengthy and extended social interaction and not in a 5min appointment slot.
So having dealt with the idea that babies can improve through the placebo effect, we move on to the question of why you think Craniosacral therapy had an effect when such an effect can't be replicated when carefully studied.
If I can recap your post briefly, your DS had colic and the beginnings of posistional plagiocephaly at age 9weeks.
After 3 sessions of Craniosacral therapy you percieved there to be an improvement (although not total) in the colic and you felt the plagiocephaly had started to improve.
Apologies if I have misrepresented you in anyway.
Now the first thing worth noting is that both of these conditions are self-limiting, that is they go away by themselves.
Following the links above we can see the NHS says that colic normally resolves by 18weeks, and 26weeks at the latest and that plagiocephaly becomes normalised by the end of the first yr.
So regardless of whether you took your DS to those sessions he would still be very likely to have got better.
And on some level, you thought that this therapy might work, however unlikely, otherwise you wouldn't have spent money on it.
Now it might be reasonable to ask whether Craniosacral therapy speeds up this progress but I hope you agree we can't tell from this one case whether that would be true.
And it strays farther from your question.
So what factors could, even in the face of chronic (that which time doesn't cure) illness could make a therapy seem to be effective when it's not.
This is a big subject (excellent if brief overview here) but it comes down to the fact that humans are not good at weighing up the evidence on these things.
We are prone to all sorts of bias and confounders and each could be discussed in massive detail which would defy anyone's patience.
But if you'll forgive me making this post even longer, I'd like to talk about two specifically: regression to the mean and mistaking correlation for causation.
Regression to the mean occurs where a chronic condition is cyclical (it goes through good and bad phases).
We have a tendency to seek help during the bad times (as you did) but good times naturally follow bad.
Assigning this improvement to the treatment effect, without considering the natural history of an event is mistaking correlation for causation.
Just because something happened after an event doesn't mean an event caused it.
These are the pitfalls humans fall into every day.
It's only by using the scientific method, a method honed to eliminate bias and confounders, can you get past them to the truth.
And it's unfortunately why an individuals experience is of little use when assessing therapies.
As a last note before I stop typing this epic post, I should point out that these same cognitive biases would predict this has little or no effect on anyone who already has an opinion.
Information that supports one's beliefs is remembered, that which opposes is rationalised and discarded.
That is very human as well.
I hope that was reasonably clear.
If I have been unclear, please post again.