Yes, a popular diesel tuner was the target a take down and fined big money for providing tunes that make vehicles non-compliant.

Omitting wear and reliability concerns, some tunes gain their effect by not controlling for things like NoX and unburned hydrocarbons.

The worst offenders? "Coal rolling". It would be one thing to do this to help spool a turbo or for some other performance reason, but it's literally running the motor as rich as possible to dump unburned fuel out the tailpipe to make a visual effect. At the expense of everyone around you.

There are few things as obnoxious and antisocial as coal rolling (open headers, maybe) and I really wish the EPA would make an example out of them.

It does, but it's worth noting that a manufacturer of such devices can make it meet federal emissions regulations (if they want to spend the $$$$ on R&D), and they can sell devices that are 100% legal in all 50 states.

Examples are Green Diesel Engineering (Who did a TON of dyno time and used to work for a major OEM on emissions stuff) and Banks (who are virtually an OEM at this point)