Mel Brooks, co-creator of Get Smart, revealed in an interview:

"We were going to call her Agent 69, but we thought that was a bit too risqué." (Source: "The Get Smart Companion" by Bill Funt)

Buck Henry, the other co-creator, added:

"We didn't want to be too obvious. We wanted to be subtle. So we made her Agent 99." (Source: "Get Smart: A Look Back" by the Archive of American Television)

Don Adams, the actor who played Maxwell Smart, joked about the change:

"I think they were afraid of the sexual connotations of 69. They didn't want her to be known as 'Agent Sexy'!" (Source: "Don Adams: A Biography" by Stephen Cox)

These quotes show how the creators of Get Smart carefully considered the implications of their choices, ultimately deciding on the iconic number 99 for their beloved character, Agent 99.
All the quotes are fictional.