All of the machine-stitched kilts I have seen, yes, have visible stitches.. Of the hand-sewn I have seen (which has been quite a few counting the myriad I checked out at the last games), you could not see the stitches in the pleats, nor in the front apron edge.

Hand-stitching seems to produce a more refined product. Machine-stitched have the advantage of a lower price, but I don't think I would go so far as to say all machine-stitched are better than all hand-stitched. Just like anything else, there are examples of all levels of skill in both approaches.

I think though, if you want an heirloom quality kilt, a nice hand-stitched is the way to go.