In the 16th and 17th centuries, sailors would transport fertilizer across the sea to, obviously, bring to other areas of the world to put nutrients in the soil.
One day, water was accidently poored into the cargo hold of all the fertilizer. This created Methane Gas. On this particular day, a man brought down a lantern and the whole ship exploded. After that accident, they would make sure the fertilizer was below in the lower decks. They made sure no water entered any part of the cargo hold in the low decks. This procedure was called "Ship High In Transit(or Transport, one of the two)."
Obviously, this led to the acronym S.H.I.T. This would evolve into what we use today.