top of the head, skull
囟 refers to the top of the head or skull, specifically the soft fontanel area in infants. It is a specialized anatomical character.
囟 is a pictograph of a baby's fontanel, the soft spot on the top of the skull. The outer shape represents the head, and the inner 㐅 marks the gap where the bones have not yet fused.
Picture a baby's head from above: the outer box is the skull, and the 㐅 inside marks the soft spot on top. 囟 is that vulnerable fontanel.
For シン, imagine a thin skin covering the soft spot: thin -> シン, and the delicate skin protects the top of the head.