I originally suspected that the safe combinations and generated randomly, and that is partly true. They are generated from a pool of, as far as I can tell, around 3 to 4 different combinations each time you play a mission (so if you load inside a mission the code isn’t changed, but if you say restart a mission the code might change).
This mission is probably the easiest out of all of them, but regardless there are a few things that will make life much easier for a stealth approach. This guide explains how to rescue emily non-lethally and undetected.
Just like the safe in this area (I have written a guide for that too, click here for it) you find this by trying to find the Runes in the Flooded District Sewers Area using the hearth. This guide explains which is the better option and how to defeat Granny Rags should you choose to do so.
The combination for me was 528, your code may be different. You find this safe by finding a Bone Charm in the sewers area in The Flooded District, in fact the Bone Charm is in the safe. Next to the safe you find a letter with a story in it.