The OP originally wrote this in the question, so I'm posting it as an answer so the question stops showing up as "unanswered":
I dealt with this for a year or so, as it wasn't super significant, it just bugged me. I use an Xperia Z5, where Sony has their own messaging app clone, which I disabled soon after buying the phone. I used hangouts before finally switching to Android Messages, where I experienced this notification bug. To fix the problem, I simply enabled the built-in Xperia messaging app, and found a sneaky unread message: an undownloaded mms image sent to me a year ago. I deleted the message and the notification bubble went away. I went back to the Android Messages app and the notification bubble didn't come back.
For those who have a pure android experience and use the default messaging app, I suggest switching to another sms app. If upon choosing said app as your default sms app, said app shows you the same ghost notification bubble, then you have a ghost message that didn't show up in the Android Messages app for some reason or other. I hope this helps a brave googler somewhere.
Temporarily switch to another SMS app. You may have a ghost message that isn't showing up in the app you normally use. Delete the ghost message and switch back.