There is no disadvantage to it. Just means you can do it now or later. No other issues concerning payment or cancellation.
There is only one disadvantage to online check-in, and this is only for RO reservations. The remaining balance will be charged to your CC on file as soon as they start up for that day usually around 6AM. So, if you have not paid off your room before check-in and you want to use GCs to pay it off, you will have to try and get them to reverse that charge. As for room requests they are getting better by offering more options, but in the past is was way to limited.
And that is why I said "if" you have not paidA way to take care of that is to get your GC and call in the payment ahead of time. You're still paying before you get there, but at least you don't have to get them to refund it.
I like online checkin simply because it's available and it's fun to have it done.