Think I figured it out. When the notification pops up, click on it. It should take you to the galaxy wearable app. If you scroll down you will see "watch connection" and it will say "disconnected." click on that... You will see "receive a notification when a watch is connected or disconnected." turn it off!
That takes me to the Gear S plugin and those notifications are off. It's driving me nuts too. I'm considering changing wearable due to this.
Although I've just gone into Galaxy Wearable under Notifications | Advanced and disabled those. Fingers crossed
Nope 2 mins later .. Samsung Gear S3, Disconnected from Gear S3.
Oh right now I'm connected again 2 mins later.
So annoying This is because I stopped wearing it during the day and it sits in my bedroom and goes in and out of range
No clue if you are still having this problem, but letting you know what I found in case it helps.
I just got a samsung watch and had the same problem. On my android phone, I went to settings > notifications > advanced > Galaxy Watch Plugin > Device Connected (and then deselected this option). No idea if the gear 3 has a 'Gear 3 Plugin' app on your phone, but it might be worth checking.
Disclaimer: I just found this setting, and I think it solves the problem, but havent tested thoroughly yet.