With regard to Rat 5 post.
Certainly when navigation was done, by using charts, nautical miles made some sense.
I recall the first a/c I flew (Forney ercoupe?) had an asi in mph.
Perhaps knots were used as they are quite a large unit of measurement rather than metres per second (if we are being strictly SI).
Maybe feet for altitude as, the alternative, metres would lead to multiples of 3 if one wanted a similar vertical separation.
I suspect though it was all to do with what had traditionally been used when long distances were covered by ships.