Online check-in on Travelnet. Question on how that relates to airport standby list

I non-rev quite a bit, and can read the numbers pretty well. But I am not sure how online check-in works for both consumers and non-rev, and maybe someone with counter or gate agent experience can explain. If someone checks in online, and then doesn't show up, which must be pretty common with positive seats and really common with non-revs, how does the gate agent know who is actually there on the flight and how many seats they have available to assign? Wouldnt the airport list counts always be off?

I am not a gate agent but generally when the flight is closed they start to call the nonrevs by their position in the priority list. The person who does not answer after several attempts loose his/her seat. I have seen in case of very tight flight pax being counted to verify if some non revs could board.
One rule of thumb with nonreving we can guess but never know until the door is closed specially nowadays...