I have noticed this more recently but I don't have 1Password installed - although it does seem like a similar issue. I checked my keybindings and I don't see anything else tied to this particular key binding as you can see below:
I've actually noticed this on a number of different character keys when using the three modifier keys I mentioned. I've also seen this issue affect some of my coworkers but with different key combinations.
I've even tried deleting Atom and reinstalling with no packages - same issue.