Do you think they could literally smell the flak?

yeah, it would be hard to smell odours from the outside when wearing an oxygen mask, not impossible, but hard. B-17 crews always talked about the pungent smell of cordite when in the thick of the battle, but then again they had some 20 .50 cals shooting, so you expect some of that acrid smell to come through the masks.

My humble experience is surely less glorious, but I happened to fly over areas with fires or more recently on fields covered in fresh manure, and trust me, you can smell that from up to 1000ft Smells tend to get more faint as u go higher, both for dispersion from winds and the rarefied air, but if the source is consistent you'd be surprised by what you can smell