I have often wondered if the Deku Butler's son story was actually meant to be clearly stated as the spirit of Link's mask, but that part was cut from the final game to save some space on the cartridge. Because hearing these little bits and pieces from the Deku Butler makes little sense on it's own. It is a story fragment that appears to lead nowhere, the Deku Butler had a son, and he is missing now. You really have to wonder just why the developers thought that little piece was worth mentioning if you had no ability to find or rescue his son. It was just some missing piece of plot that happens to be there, and for no other reason then to have the Deku Butler say it.
Normally a quote like this would lead to another miniquest to go find the son of the sad character. Or at least do something to console the saddened individual, but no. This entire plot point is never mentioned again in the game. Even the racing minigame with him mentions him racing his son the same way also hinting at Link taking the form of his son.