With 1/2" sheathing the nail is required to penetrate through the sheathing. With a 1X4 (3/4" thick), the nail is required to penetrate to the lower surface. See the ICode section below. A 3/4" roof nail won't be long enough to meet the IRC requirement and probably the shingle manufacturers requirement. I'd take the nails sticking out any day. R905.2.5 Fasteners. Fasteners for asphalt shingles shall be galvanized steel, stainless steel, aluminum or copper roofing nails, minimum 12 gage [0.105 inch (2.67 mm)] shank with a minimum 3/8?inch (9.5 mm) diameter head, ASTM F 1667, of a length to penetrate through the roofing materials and a minimum of ? inch (19.1 mm) into the roof sheathing. Where the roof sheathing is less than ? inch (19.1 mm) thick, the fasteners shall penetrate through the sheathing. Fasteners shall comply with ASTM F 1667. Tom Corrigan