The character appears to be awake in my watch list, but for some reason, it didn’t appear on the awake list. I could not message the person.
That was actually just me being sneaky! 
I was using the "hidden":true setting that bots can use to prevent them from showing up in the Awake list. While primarily for bots, it can be used by admins too.
The feature was introduced in Release v1.51.1. And while it doesn’t technically (server side) prevent messaging, the command console relies on the awake list to lookup valid message targets. So, messaging becomes tricky, yes.
Normally, when I take care of things without wanting to draw attention, I use some alt. This time I needed to use my main character though.
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How do I enable it for my character?
It can only be used by bots and by admins. For bots, you choose if they are hidden when calling wakeup:
Example in Javascript
botChar.call('wakeup', { hidden: true });
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