What is the name of the traditional Irish and Scottish leather shoes worn over thick wool knee socks?

Ghillie brogues, not ghillies. A Ghillie is the old gaelic term for a servant that accompanied someone on a hunting or fishing trip.

Wood, The ghillie that you are talking about as the servant is derived from the Scots Gaelic "gille" meaning "boy". The "h" in the word is used as lenition depending on how the word is being used, for example in the dative case. This is the same reason you see variants of names like Mairi/Mhairi.