The thing to remember as that in almost all cases, the skeg is not used all the way down. Most of the time, just cracking a skeg down a half inch or less will stiffen up tracking enough to do the job. People sometimes use a skeg down all the way for surfing. You will feel a difference in hull speed with it all the way down. Not a lot, but definitely noticeable. As far as how much drag the hole causes, only real testing would answer that but it would not really be that noticeable.

Unless you're air-borne, the skeg stays in the water.

If you have a boat that is getting pushed all over the place or weather cocking, and you have to constantly correct, the trade for ease of control is far worth any negative speed loss.