Long ago, a come-along was a type of shive used in dredging*, it floated on a long line until pulled via a second line, and then dogged into the long line so you could pull the long line with the short line, then when tension was released, it slipped back along the long line and you could start over and do it again.
With a pair you could pull yourself along a tow line, or pull in a long dredge line without using a winch with a huge quantity of line on it.
I suspect, the term came from there (A short hand winched line would be a reasonable improvment for some applications...) ... speculation on the latter tho...
*the original design is somewhat similar to power line pullers.