御 -go is a suffix, distinct from the prefix go-. The suffix is used to show "light respect" towards human beings only, mostly after family terms (so not for general nouns like go-Iken, etc.). The Kokugo Daijiten dictionary attributes it to an abbreviation of 御前 Goze.
Goze, Gozen was originally a word for nobility, then a respectful term for adult women, then a respectful term of address for women (a treatment pronoun). By the 13th century we see -goze used as a polite suffix; in the Heike Monotagari (Tale of the House of Taira) we have characters addressing others like やや副将御ぜ Yaya, Fukushō-goze… “Well now, Lord Vice-captain…”
In the same work we have the first known appearance of -go as 母御 (modern Haha-go). By the time the Jesuits came and described the language, around 1604, they found it in use for the whole family: Faua-go (Fawa-go, modern Haha-go), Tete-go (father), Vôgi-go (ヲウチゴ Wōdji-go, modern Ojī-go, grandfather (not Ōji, prince)), Ani-go older brother, Vototo-go (Wototo > Otōto), Vba-go (Uba-go > Uba), Vôba-go (Wōba ?> Obā), "&c.".
The Jesuits explain of -goien (gojen = ごぜん; ぜ was like じぇ at the time) and its reduced form -go that:
The first particle of these two [=ごぜん] is proper solely for women, & honour them in the manner of Sama, out of respect for the noble people to whom such women belong. […] -Go [, by contrast,] is proper for men & women.
Notice that this is already different from the use of -goze to address the captain in the Heike. Apparently the longer form became sufficiently associated with women that the shorter -go replaced it as a gender-neutral suffix.
- Kokugo Daijiten.
- Arte da lingoa de Iapam (my translation).