Sure is odd to have a very public piece of infrastructure get erected over and over and yet not get an explanation about what it is.
They likely house a level of chemical-sniffing technology too, like police cars can be equipped with (http://www.inficon.com/). These sniffers would likely be actively looking at emission levels etc (being near tunnels would provide a reason for that), however can also detect explosives etc.
http://gothamist.com/2017/09/26/towers_mta_gateway_cuomo.php