They act as natural choke points since Manhattan is an island.

In turn, that means that you know who entered or exited Manhattan and can therefore deduce who is currently still there.

I would imagine in the event of an incident related to a vehicle, you could start with the list of recent entrants and use it to start building a timeline.

Wild speculation: Bridges and tunnels are more sensitive infrastructure, this is done for security reason. In case of some kind of emergency they could tell how many people/who might be in there. Collect data on usage that might be relevant to the unique maintenance needs of bridges and tunnels. On an island like Manhattan, for example, bridges and tunnels represent many of the ways in and out, so would be natural places to surveil for various reason.

I assume that's where the scanners are mounted.