I thought the military had exemptions on EPA compliance for stuff. For example: US Army tanks use depleted uranium projectiles. Those are definitely not good for the environment.
The military must follow all EPA regulations as a general order, but someone at a high enough rank in the pentagon can make an exception for a specific rule/reg.
I'm scratching my head as to why someone in the pentagon wouldn't do this for hull maintenance on seagoing vessels. It seems rather important.
Probably because the chemicals they were using are pretty nasty and were used in high volumes. They were doing a lot of damage to the environment and there are alternatives. They just haven't been approved yet for use by the navy. It's not a good look to continue using damaging, outdated methods because your bureaucracy is so bad that can't utilize new technology.