I guess I've based my assumptions on the only plane I've ever seen popping flares, which was an old Sukhoi. From what I've seen in old school textbooks, a lot of those planes had flare dispensers aimed upwards. Maybe the idea is that ideally they would try to get a side aspect to the missile either way, so it wouldn't matter as much?
Now that you mention it, newer MiGs - I mean as new as a MiG-21 is - drop flares downwards. I'd love to find out more about the engineering of this.