We've discussed this kind of thing before. Not certified does not mean not capable, not safe, or not possible. It just means that the equipment hasn't met a set of performance, handling, ergonomics, etc. specifications that the airworthiness authorities have said must be met. We have airworthiness to make things safe...its not a bad thing.
With aviation, the markets are small and the testing can be expensive. I'm not sure why the Bell 412 with nightsun isn't IFR certified, but I wouldn't be surprised to hear that cost is a big factor.
I'm not surprised that some are flying that configuration. I don't know what the outcome would be if there was an incident, but I imagine the insurance companies would consider everything. Even more importantly, if you can trust that the specifications have some sort of validity, then assume that any configuration not tested has the potential of failing, it is possible that the configuration is truly unsafe.
For the Bell 412 with the nightsun there may be some handling problems following an AFCS failure, OEI performance issues (ie not being able to meet IFR climb gradients), electromagnetic interference issues, etc. Just because some are flying with it, doesn't mean that they've seen all the conditions required for certification.