Hi,
When I checked the Apple ID site a little while ago and looked at the devices it did tell why some might appear in the list.
Check your Apple ID device list to see where you're signed in - Apple Support
It seems that some can be listed if they use a linked email in one app that is not used elsewhere.
For Instance I have my Original Apple ID which is based on a Dial-Up service I once had.
When iCloud came out I linked it to iCloud and got an @me.com email as well and later an @iCloud.com one as well.
For some things I can use them independently.
I tend to use the @me.com one for iCloud on the iPhone, Mac and iPad.
I use the original Apple ID in the iMessages Account on the same devices.
I could add another iPhone to the set up and use just the Original ID and not worry about linking it to iCloud.
This iPhone would then appear in the list of devices even though only one app was using the ID.
Whilst my set up of using different parts of the Apple ID/iCloud ID I could also see that you might have only set up Messages on your Mac.
I am trying to find out if my two older computers that don't have software to do iCloud will show up if I restart up iTunes.
I am stuck at the moment I as cannot remember one of the answers to one of my Security questions.
If you have had two Step Verification since 2014 has the Mac and it's version of Messages been logged in all that time ?
I don't use it myself but my understanding is that if an app is logged in at the time it is set up the Precess of needing an separate Password for that app does not happen until it needs to log in again.
I notice that there are not ways of deleting an ID either.
The way to add a device is to use an ID that is linked to the iCloud ID on a device and it should appear.
Currently as I said above I am trying to check in my MacBook Pro will get added now I have Logged in via iTunes

7:47 pm Wednesday; February 17, 2016
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad