Yep, definitely trying to prepare interesting complications that are suited to a stealth-based mission.
But there's also a point where those two things meet – actions the players might take, and presenting interesting complications. In order to be interesting, the complications I present need to be meaningful challenges based on the PCs' capabilities and strategies/actions the players lean towards. A DM needs to think of both, right?
I think it's easy to fall into thinking that way, but I also think it's not necessary and sometimes actively unhelpful (such as spending time on prep that gets set aside because the players don't do the thing the DM imagines they will do). A solid list of complications, some idea of when the overall challenge is won or lost, and a bit of nimbleness on one's feet is what I would lean on here.