Check-in is the act of confirming you have arrived, whether at a booked desk, a meeting room or the front door as a visitor. It sounds small, but it is the mechanism that keeps booking data honest.
Without check-in, a booked desk that nobody uses still looks occupied. With it, unclaimed bookings release automatically for someone else, and your utilisation numbers reflect reality.
Check-in features vary a lot between tools; the best visitor management systems comparison covers who does it well.