1 Samuel 16:7 contains God's statement to Samuel when he was looking at Jesse's sons for a king: "the LORD seeth not as man seeth; for man looketh on the outward appearance, but the LORD looketh on the heart." The word for 'heart' here — levav — encompasses the whole inner life, including the physical interior of a person. God's vision is specifically different from human vision in that it does not require visible evidence to register reality. The invisible illness is not invisible to him.
Psalm 139:1–3 describes a God whose knowledge is comprehensive: "Thou knowest my downsitting and mine uprising, thou understandest my thought afar off. Thou compassest my path and my lying down, and art acquainted with all my ways." The Hebrew word yada — 'knowest' — carries the sense of intimate, experiential knowledge, not just factual awareness. God knows the specifics of a body that is suffering in ways no one else can see.
Commentary is from a charismatic Protestant perspective, drawing on KJV text and public-domain sources including Spurgeon, Andrew Murray, and Matthew Henry.