Just spotted this old thread.

I have assumed that the cabin boy also carried a wire saw, drilled two holes above the waterline and one below, in a sort of inverted triangle two or three feet across, and threaded the wire saw through each pair of holes and cut through.

As it says in what's surely my favourite version of the ballad:

"He took his little auger and he bored it once or twice
Then he bored for a third time with that little neat device
He made an inverted triangle, which you might have said looked nice
And he sank them in the lowlands low.

"Yes, he made an inverted triangle of holes that were so deep
One in air, two in the water, on the hull that was so steep
And through and through those little holes the water began to seep
And he sank them in the lowlands low.

"Then he sawed with his wire saw, the best that he could do
He ran his saw right through the holes and sawed the hull all through
It only took that boy an hour, or maybe it was two
To sink them in the lowlands low.

"O some were playing card games all of their own invention
And some were in their hammocks doing things I will not mention
But whatever they were doing, it took up their full attention
While he sank them in the lowlands low."