Let me start off by saying no aftermarket ECU is OBD2 legal. You can get a very stiff fine no matter what ECU you choose to run if you get caught.
With that said the Hydra EMS does not have OBD2 so nothing will show if an OBD2 reader is plugged in. I have heard of some playing stupid and a tail pipe test was substituted. All counties are different in regards to OBD2 testing or emissions. For example I had a car get an exemption because it was too low to drive over the dyno rollers
What I did with my Hydra equipped car to pass the OBD2 test was to reinstall my catalytic converter, stock injectors, and OEM ecu. I drove under 60% TPS on the highway for about 30 seconds above 50 mph, pulled over, turn off the car, and repeated 4 times. This set all my readiness codes except one. In MD you are allowed to have one readiness code "incomplete" and pass. I took it straight to the testing center and voila passed.
I would say this whole process took about 2 hours to install a cat, oem ecu, and oem fuel injectors (STI side feeds are great!). To do this once every two years to ensure I have the best possible ECU for the level of modifications to my car is well worth it.
I have heard from my other customers that they just run a "big MAF" so they don't even need to swap the injectors.
Hope this helps.