For hand quilting, historically it has always been done 1/4" to the side of the seam. There is no point doing hand quilting in the seam, as it wouldn't show up!
Machine quilters do it in several different ways, including 1/4" to the side of the seam and right in the seam. Machine piecing is not as fragile as hand piecing, so machine sewing in the seam typically isn't a problem (because the quilt has also been machine pieced). I would never machine quilt over the seam of a hand-pieced quilt, as it could break the piecing thread.