First of all, it’s better to refer to it as Eve’s World; Martha is a character common to both worlds, whereas Martha growing up into an old women who goes by the name Eve is the unique characteristic of the world you’re talking about.
But to answer your question, the reason why Jonas does not exist in Eve’s World is that Mikkel never time travels to the 1980’s, so he never marries Hannah and thus Jonas is never born. Why does Mikkel not time travel? Because he doesn’t go with the older kids to the cave on November 4, 2019. Why doesn’t Mikkel go to the cave? Because he’s old enough to not need a babysitter, whereas in Adam’s world (the main world seen in the first two seasons) he was younger so Martha and Magnus needed to take him with them.
So ultimately the difference between the two worlds stems from when Mikkel was conceived; he was conceived earlier in Eve’s World than in Adam’s World. Why the difference? The show doesn’t address that, but one possibility is that in Adam’s world, Mikkel’s presence in the 1980’s somehow caused Hannah to observe Ulrich and Katharina, leading to her falsely accusing Ulrich of rape. And the awkwardness of a rape accusation might have delayed Ulrich and Hannah’s eventual marriage, and thus their conceiving of Mikkel. Whereas in Eve’s world, in the absence of Mikkel’s presence in the 1980’s Hannah might never have observed Ulrich and Katharina, and in the absence of the rape accusation Ulrich and Katharina’s relationship might have progressed to marriage and children more quickly.