Despite all of the choices that Deus Ex: Human Revolution gave the player, the different endings were not reflected when going into the sequel. This is why it left things vague and open-ended so that players could reasonably feel like their decisions were represented in the sequel, without actually honoring their specific choices concretely.
However, it looks like that approach will be changing with choices in Mankind Divided and how things play out in a potential sequel. Producer Olivier Proulx spoke with Finder about the lack of impact in choices from Human Revolution to Mankind Divided, blaming the lack of technology as the reason that such a mechanic was not implemented.
He goes on to say that “As for this new game, we don’t know whether there will be another Deus Ex game or not. However, we are tracking your choices and the consequences in Mankind Divided. When you’re done, we seal your save game file with everything that you’ve done and that’s gonna give us the option in the future. If we’re lucky enough to work on a sequel, we can use that as a stepping stone for you to come in and continue where you left off. So we have changed our approach to tracking your progress.”
This doesn’t confirm that there will be a sequel, but considering the success that the series has had so far it would not be all that surprising if there was. Deus Ex: Mankind Divided will launch for PlayStation 4, Xbox One and PC on August 23rd.