This example is very informative: 00:29 -!- xiaomiao is now known as bonsaikitten 00:29 <+bonsaikitten> meow. 00:29 <+willikins> bonsaikitten, you have notes! [00:26] <wiktor_b> I got it working. 00:29 -!- bonsaikitten is now known as xiaomiao FreeNode allows you to spend 30 seconds under the nick of any registered user, if its offline. Willikins seem not to check whether the user is logged in. Even if !note is not a feature used to transport private info, you can still use it to prevent the receiving side from getting the note.
You probably shouldn't rely on an IRC bot to convey important messages, and noone in an official capacity does so to my knowledge. We use the plain note functionality from rbot, willikins' base code. So, if you want this fixed, contact upstream; we don't have the resources for this.