The general idea is that if you sew all the way through the suit you will create a bunch of tiny leaks. This might not be a big deal on a 3mm suit in the tropics, but could make a difference in colder water.
Also a good point. But "through" rather than "blind" hand stitching can also irritate waterlogged skin, especially on liveaboards in the tropics where you often don and doff the suit 4-5x/day. It can make a difference, especially if you are also a little sunburned.