Since the "means by which" is uncountable (craft) then the plural should be the same as the singular; i.e. one craft, many craft. This also applies in English to older agglutinates like aircraft. Newer agglutinates (for example laptop) are far less likely to follow this rule; one laptop, many laptops.
English, due to its muddled heritage and well intentioned but half informed linguists over the years, is a very messy language.
I think for river travel it was common to build a boat/raft to make a journey and then break it up at the destination. In that context maybe the object of the boat was secondary to the act of making the boat. And at some point boats became more personified and thought of as things in their own right.
