Strength: An assembly with three socket head cap screws has more strength than one with five equivalent hex head screws.
Savings: Using fewer screws means labor savings associated with drilling fewer holes and installing fewer screws.
Tensile, yield, and shear strength: An assembly done with a cap screw has over 50% more tensile strength, 100% better yield strength, and over 30% more shear strength.
Clearance: Socket head cap screws have no side clearance restrictions associated with the sockets and wrenches used with hex head screws. As a result, they can be placed closer together, and used in applications where associated side clearance would make hex head screws impractical.
When overhead clearance is an issue, or a flush profile is necessary, the low head and flat head versions are a good solution.