The NCIS mission involves protecting the people, equipment, technology and infrastructure of the U.S. Navy and Marine Corps. Once it was discovered the sailor was not the target of the bombing, the entire case would be handled by the NOPD and or ATF/FBI. The NCIS investigation would be limited to the death of the sailor.
When the agents find the second device, they make two significant errors- opening the seat where it was located, and then the other one using a radio to communicate. Radio frequency from a nearby transmitter can set off an explosive.