In the 16th and 17th centuries, everything had to be transported by ship and as it was also before the invention of commercial fertilizers, large shipments of manure were quite common.
Several ships were destroyed in this manner before it was determined just what was happening.
After that, the bundles of manure were always stamped with the instruction ‘ Stow high in transit ‘ on them, 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 ‘, (Stow High In Transit) which has come down through the centuries and is in use to this very day.
You probably did not know the true history of this word.