I think the external BB is definitely easier to deal with, and they're supposed to be more ridged and weigh a little less. All you need for crank and BB removal is a hex wrench and a pair of channel locks. Square taper requires 2 special tools. If I ended up having to overnight a replacement BB for some reason, I'd rather it were an external that only requires basic tools that a small town is more likely to have(You'll probably have a hex wrench, but not channel locks). I'd also think they're less available since the good ol' square taper was in use for soooo many years. Lots of them are still around, new and used. That's the route I'd go if I were touring in another part of the world for a very long time. At the same time, how long are you going to be in South America? If you get an external BB now, I'd think it'll last a couple years until you're done with that trip. If you don't take that trip for several years and your BB is starting to feel less than perfect by then, just put on a new one before you go. A perfectly decent Shimano BB only costs ~$30. And there's nicer stuff available of course if you want it. Plenty of mountain bikers manage to put a lot of tough, dirty miles on their standard Shimanos, though. I wouldn't worry too much about it.

EDIT: Oh, and if you go external, I'd stick with Shimano. I'm not sure about particular the area's you'll be heading, but they're the most popular overall.