A period already does suggest a pause. I wouldn't think that even an em dash would necessarily suggest a longer pause—although it's subjective how each person interprets the cadence of a sentence.
If you finish the first sentence with a question mark that will also indicate a pause—possibly one even longer than just a period:
You maybe wondering how that could be? That she is considering to run away?
It's true that this turns it into a direct question. But it seems unidiomatic to me that these two sentences should mix indirect and direct questions in the first place.
If I think of hearing somebody keeping their voice level with the first sentence, and raising it with the second sentence, it doesn't sound right. (Unless a shorter pause is used.) But raising their voice after each sentence—or keeping it level—seems more appropriate:
You're maybe wondering how this could be. That she is considering running away.
Note, too, that the second sentence is actually a sentence fragment rather than a fully independent clause—but that can be fine in fiction, informal writing, or dialogue.
As referenced in another comment, an ellipsis could also be used. But that's just a matter of style.
Still, in all possible answers to this, it will be a matter of style (and subjectivity) rather than anything certain.