I think the numbers follow the old and new ways of counting in Japanese. I don't get it entirely myself, but it goes like this:
Old: Hi, fu, mi, yo, itsu, muu, nana, ya, kono to
pronounced: hee, foo, mee, yoh, itsu-oo, moo, nana, yah, koh-noh, toh
New: ichi, nii, san, yon/shi, go, roku, nana/shichi, hachi, kyuu/kuu, jyuu
So then...
Gokudera=59: Go=5 Ku(kyuu/kuu)=9
Mukuro=69: Mu=6 Ku(kyuu/ku)=9
Have a list:
Vongola
G = Giotto
27 = Tsunayoshi Sawada
59 = Gokudera Hayato
80 = Yamamoto Takeshi
18 = Hibari Kyouya
L = Lambo (L is oftentimes used to describe Lal Mirch as well, causing confusion. I've seen someone describe Lambo as L8 to create separation, but it's not official.)
84 = Basil
Cavallone
D/Boss = Dino
Kokuyo
594 = Kokuyo
493/193 = Chikusa
69 = Mukuro
96 = Dokuro
Acrobaleno
R = Reborn
56/C = Colonello
Varia
3/X = XANXUS
39/S = Squalo
Millefiore
100 = Byakuran
51 = Irie Shouichi
48 = Spanner
Ten Years Later (basically just adding a 10 before the normal character number)
1027 = TYL Tsuna
1059 = TYL Goku
1080 = TYL Yamamoto
1069 = TYL Mukuro
1018 = TYL Hibari
Other
86 = Haru
87 = Hana
And that is the extent of my knowledge on the subject. :>