Funny how that is not a problem in DL or TDL where the canoes, keel boats, Mark Twain (and in DL's case - the Columbia too) could all work together for decades.
I suspect it is two fold - 1stly the bad behaviour of many guests with linguistic barriers causing an issue, coupled with a cost cutting measure = no more canoes. The reason they disappeared in WDW (and for a very short time in DL) were to save on the cast members and insurance overheads.