Disclaimer: I'll use the word 'relationship' in the general sense, encompassing any kind of relationship; I'll use the term 'exclusive relationship' to refer to, well, an exclusive, mutually agreed to relationship.
So, let me recap. He told her he doesn't want to be in an exclusive relationship; he wants them to be friends, and he want to have sex with her occasionally, but also wants to be free to have sex with other women. So far so good.
In return, she told him "that he must tell her as soon as he has something with someone else, and then she'll end it." This does not sound like she agreed to have a friendship with benefits; it doesn't even sound like she fully understood what he was trying to tell her. It sounds like she thinks they will have an exclusive relationship which will end the moment "he has something with someone else" (and I'm not even sure what exactly she means with this term - the moment he has an interest in someone else? The moment he has sex with someone else? Does your son know?).
As he has asked for your advice, he clearly understands that there is a misunderstanding between the two of them, and from this misunderstanding springs his insecurity about how to proceed further. So obviously, the first step would be to go back to her and try to clear up this misunderstanding.
If he succeeds in clearing up this misunderstanding, she will probably make the decision herself whether or not she wants to continue the friendship, and under which terms. If so, the case is solved and he can move on.
If the misunderstanding persists, or even if she says that she has understood but then continues to contradict this by other things she says (like what you quoted above), then your son needs to decide how he wants to proceed, and I'll try to describe the consequences that I think will be most likely to occur.
should I try to make clear to her all the time, that we are not together, so when I actually meet someone else, the final punch in her face will be less brutal or should I say/act not related to this and one day surprise her with the news that I was with someone else?
So, once your son did his utmost best to clear up the misunderstanding, her decisions are obviously her responsibility. But as you have written above, your son actually cares for her, and doesn't want her to get hurt. Of course he's not responsible for her possibly making wrong decisions, but his actions will affect her, which in turn will determine the course of their friendship. If she continues to send mixed signals and he continues to suspect that his and her interests aren't aligned, he needs to decide what is more important to him. His options in that case would very likely be:
- have sex with her, have sex with other women, and risk her getting hurt and end the friendship
- decide that he values their friendship (without benefits) more than he values having sex with her, and seek out other women
- agree to an exclusive relationship (which he's probably not interested in doing, and that's fine)
I don't actually think that it makes a difference whether or not he tries "to make clear to her all the time, that we are not together" - he needs to make sure he did his best to clear up the misunderstanding, but if she doesn't understand then, telling her every day won't make a difference.
I really like her, if I have something like a one night stand with another girl, I don't want to lose her for that. What if I just keep it to myself?
Seriously, this isn't that hard.
Ask him to imagine he has one night stands with other girls, and keeps it to himself. He might be able to hide it for a few times, but sooner or later he might have to lie about it. Does he want to be that kind of person?
Also, as it stands now, she agreed to the (possibly not well understood) relationship between them under the condition "that he must tell her as soon as he has something with someone else, and then she'll end it". If he has a one night stand with another girl and keeps it to himself, despite her specific request, it means he's disregarding the terms under which they agreed to this relationship, and she has every right to feel betrayed.