I found this info on a KND fansite, and I'm not sure it's true or not, but it's pretty good logic, anyway.
Numbuh One - His name is Nigel Uno. Uno means "One" in Spanish.
Numbuh Two - His real name is Hoagie P. Gilligen Jr. Jr. means he is the 2nd persond to have that name. 2nd = Two
Numbuh Three - Her name is Kuki Sanban. Sanban is the Japaneese word for "Three"
Numbuh Four - His name is Wallabee Beetles. The old but famous rock group, The Beatles, originally had Four members.
Numbuh Five - Her name is Abigail Lincoln. President Lincoln is on the Five dollar bill