The primary defence is to keep the water out of the housings, using sealed ferrules of some kind, (or having the top end of the cable housing run facing downwards or something). The lube in the cables makes a big difference too. An absolute no-no is to have a cable housing run which is both open at the top and has a low point/ loop in it (eg under the bottom bracket) which can allow water to pool inside. Even the gentle run down the chainstays of an IGH cable can allow water in (forwards) and this is a common cause of IGH cable problems.
Absolutely this.
I consider cable outer to be a yearly consumable on recumbents with underseat steering and folding bikes that get exposed to significant rain. Once there's water in a cable loop, it's on borrowed time.
Things I've found that seem to help on bikes where such loops are unavoidable:
-Taping up the slot in the leading edge of MTB brake levers to keep rain from being driven at the open end of the cable.
-Greasing the inner where it emerges from the outer.
-Boots and careful choice of ferrules.
-Riding with my hands covering the bar-end shifters on USS bars as much as possible when caught in a downpour.
-Putting a bag over USS controls when parking the bike outdoors.
-Flushing the outer through with lube once symptoms start to occur (an oil port helps with this)...
-...but not being shy about replacing the outer when it inevitably deteriorates. Having a bulk roll of the stuff to hand helps.
I haven't found an appreciable difference between pre-lubing cables and installing them dry.
I've had a couple of teflon coated inner cables (came with bikes) and wasn't impressed. I found much of the coating had rubbed off the cable when I removed the working cables to change the shifters.
