1) One individual had a bullet as a child go right through the left temporal lobe.
2) I had my kids go to bed.
I think '2)had' is 'commend', but I don't think '1)had' is.
then, What does '1)had' mean?
You are correct about #2; had can mean "caused" or "commanded". See definition 6 here.
In sentence #1, the meaning of had is "experienced": he experienced a bullet through the left temporal lobe. See definition 4 here:
4. to experience, undergo, or endure, as joy or pain: Have a good time. He had a heart attack last year.
I think the sentence is not very well-structured, by the way, because "as a child" modifies the individual, not the bullet! It would read better as
One individual had, as a child, a bullet go right through the left temporal lobe.
One individual as a child had a bullet go right through the left temporal lobe.
As the sentence is, it's a little bit of a garden path sentence, one that tricks the reader into thinking it means something else until more later in the sentence when the reader realizes he has to go back and re-interpret the sentence.
One individual had a bullet as a child...
looks like one individual possessed a bullet when he was a child, but then we read
...go right through
and we have to go back and say, "Oh, it means experienced, not possessed."
The first "had" means that the event happened to them, as in the construct "I had something happen to me when I was four". It can also be used in the future tense (e.g. "I will have my tires checked tomorrow"). I am no language expert, but I think this is used when the subject ("One individual") has things happening to them passively. This does not necessarily mean the person did not cause the things to happen (as your second sentence means effectively "I have made/asked my kids to go to bed".
This also means that in most cases you can rewrite the sentence to an active form:
"A bullet had gone through one individual's left temporal lobe when they were a child."
The bullet becomes the subject instead of the individual.
Note the usage of "they" as the individual's gender is unspecified. There is some dispute about such usage, but it is fairly common.