The reason you see both of them in the console is because Super+S is not bound to any command yet; so after Sublime tries to see if anything is assigned to that key and it’s not, it drops the super modifier and tries the new key sequence again to see happens, which results in it trying to use just s as a key. You will notice that when this happens, an s is inserted into wherever the cursor is currently located (maybe your document, maybe the console input, etc).
Curiously, this only seems to be the case for the super modifier when used with an alphanumeric key. You’ll notice that if you try Super+Shift+S you get a similar result, only now the second key event is 0x53 (upper case S) instead because it dropped the super and is trying again with the rest of the modifiers. However Super+F11 only shows the first sequence. This is probably because of the special nature of the super modifier, but that’s just a guess.
In any case, if you make a binding to the appropriate key by itself, Sublime will stop when it finds the mapping and the second one won’t appear. For example, by default I see this:
>>> sublime.log_input(True)
key evt: super+s
chr evt: s (0x73)
(and an s appears in the console input)
If I add this key binding:
{"keys": ["super+s"], "command": "echo", "args": {"msg": "I am the key"}},
The console output becomes:
key evt: super+s
{'msg': 'I am the key'}