In the 16 and 17th centuries, everything had to be transported by ship. It was also before commercial fertilizer's invention, so large shipments of manure were common.
It was shipped dry, because in dry form it weighed a lot less than when wet, but once water (at sea) hit it, it not only became heavier, but the process of fermentation began again, of which a by-product is methane gas.
As the stuff was stored below deck in bundles, you can see what could (and did) happen. Methane began to build up below decks, and the first time someone came below at night, with a lantern, BOOOOM!
Several ships were destroyed in this manner before the cause was determined.
After that, the bundles of manure were always stamped with the term "Ship High In Transit" which meant for the sailors to stow it high enough off the lower decks so that any water that came into the hold would not touch this volatile cargo and start the production of methane.
Thus evolved the term "S.H.I.T.", which has come down through the centuries and is in use to this very day.