The only other thing I could think of is that long barrels make it more difficult to aim and shoot accurately with one hand while on a horseback, hence the choice. This of course has nothing to do with water resistance.I noticed the same, but my understanding was that that was about specific duelling pistols in comparison to other pistols, not long guns. They had a more refined trigger mechanism to increase reliability and reduce delay between pulling the trigger and the shot firing. I also found some other source that mentioned waterproofing, but again, that was on the firing mechanism, and had nothing to do with the barrel.
Though the set up of the story seems to be fine: their rifles (v1) are not water resistant and so the opposing general waited until it rained before attacking; Ike wanted to waterproof the firing mechanism and at the same time chose to turn it into pistols so the cavalry can use it.
And so, I’m leaning towards the author/artist goofed up on the dialogue. Or perhaps as @BlackAeronaut mentioned a translation issue...?