The simple answer to the question is protection from enemy fire. Over the centuries, defences ranged from earthworks, timber palisades, wooden forts, castles, citadels etc. As the power of weaponry increased, and new weapons were invented, new methods of defence needed to be developed to counter their effect. Fort Siloso was just one small part of the progression of defensive systems.
Roman troops had their Ballista and Manganum catapults which fired large arrows and stones respectively. Pots of tar were set ablaze and fired from Manganums as incendiary weapons. The Roman army made very effective use of these primitive artillery weapons against a range of defences. When ammunition was short, they would even fire stones or the heads of captured enemies into defensive positions. In medieval times, Trebuchets and Mangonels, were used to hurl heavy rounded stones against and over the walls of castles and other defences.
By the 14th century, muzzle loading cannon reached the stage of development when they could be effectively used against castles, Trebuchets and similar devices were abandoned in favour of cannon, although there are records of them being used for many years after that. Cannon outranged Trebuchets and the archer, who could outrange a Trebuchet and bring fire down on the men working them, putting the new artillerymen safely out of range. Cannon also had more hitting power than their leverage predecessors. Castles and other fortifications were now very vulnerable, and in North Wales, one solitary cannon was used to end the siege of a castle. New defences against the power of cannon were needed and rapidly developed.
New castles were built with a lower profile, the high curtain walls of old castles being too vulnerable to cannon fire. These new castles, such as Southsea had much thicker walls, and were surrounded by a large deep ditch or moat. The battlements only protruded high enough to provide a field of fire for the defenders artillery and other weapons. Southsea Castle was built by King Henry VII in 1544. Other new style defensive positions consisted of massive earthworks faced with stone and surrounded by ditches, some water filled. A fine surviving example is Berwick-upon-Tweed in Northumberland, England. These fortifications were built by Queen Elizabeth 1st in 1558.
By the time Fort Siloso was constructed, it was considered good practice to build underground. It was also, by this time well known that earthen emplacements or coverings were good defence against both solid shot and explosive shell. By building stores, magazines, generator rooms etc., underground, there was therefore excellent protection from enemy fire. The only fighting parts above ground were the gun emplacements and fire-control systems. Other buildings above ground were not essential to the fighting capability of the Fort, and it was not deemed essential to provide them with protection. Within a few decades, Fort Siloso itself was outdated. Fixed defences were easy to target by aircraft, and heavy bombs would be able to penetrate the underground areas. In the Second World War, the Royal Air Force destroyed German Submarine shelters in France with 5,000Lb bombs which went straight through several metres of reinforced concrete before exploding in the shelters. Larger bombs of 22,000Lb were also used by the British with devastating effect on other difficult to destroy targets.
Underground fortifications were used in Borneo by British forces in the 1960s, and by the American forces during the Vietnam War. Fire bases were constructed in jungles areas to provide accommodation for infantry soldiers, and a base for field guns. The two photographs above are of British jungle forts in Borneo, On the left, Red 19 (name forgotten) and on the right Red 345, Gunong Gajah. Both were in the 1st Division of Sarawak. All the major accommodation is underground to protect it from mortar fire, and an area around the forts has been cleared to provide a field of fire.