Base64 encoding does protect somewhat against "looking over your shoulder" attacks

(Unless the person looking over your shoulder has a really good memory and can remember the Base64, or decode it in their head. Or they have a camera.)

Helps against attackers grepping the whole disk (or any folder named "conf" or similar) for "username", "user", "password", "pass", "key" and friends.

It's game over anyway if someone has a shell on your server but at least it complicates their life a bit.