This is not true. The article you linked only mentioned one particular instance that the battery fire was not the result of a e-bike battery. There have been fires due to bad e-bike batteries (see https://www.thecity.nyc/2022/11/21/ebikes-fires-lithium-ion-..., and https://www.thecity.nyc/2024/01/31/ebike-battery-fire-hazard...).
I'm a huge pedal assist e-bike fan and I use my e-bike all the time around NYC. Throttle based e-bikes used to be technically illegal in NYC until 2020 (pedal assist were not), which is what all the delivery workers still continue to use. (https://www.nyc.gov/html/dot/html/bicyclists/ebikes.shtml). Do you have a citation that they continue to confiscate e-bikes?