I've been unable to do online check-in a number of times and it's almost always due to travel documents - the system didn't like what I provided for some reason and wouldn't let me check in until a human at the check-in counter confirmed I did in fact have the appropriate visa, etc. Never got an SSSS in those situations but it did sometimes take a tad longer to check in. Not a big deal, but either way I'd just get there a bit early if you're concerned.