It's a standard naval phrase used all the time in British heritage navies for hundreds of years. It was common practice when I was in the Royal Canadian Navy for over 20 years. It's used officially when it is time for an action to occur, but requires the senior officer present to issue the order and officially begin the evolution. For instance at sunset, the officer of the day is advised "sunset sir/ma'am" and the officer looks at his watch and says "very good, make it so" allowing the ritual to begin and initiating the evening watch routine. It's also used for other things, officer of the watch advises the captain "there is a contact on our track recommend we alter course 10 degrees port to avoid" the captain looks down the track, nods, and says " yes, very good, officer of the watch, make it so". As a classically trained actor who has played British naval officers prior to Star Trek, Patrick was aware of the common phrase and used it in an ad lib. It seemed to go with the Brit accent, writers liked it and it stuck.

Also "Number 1" is British naval slang for the First Officer or XO, it is comes from the days when the senior Lieutenant on a ship was the First Lieutenant, or the Lieutenant Commander, and therefore usually second in command. Also called "Jimmy the One" or "the Jimmy". On a larger ship where the XO is a Commander rank, the position is still often referred to as 1st Lieutenant.