Sorry for your inconvienience. Sounds like you didn't handle the situation properly. You should have made Mazda fix the problem, even if your OBDII system didn't function properly. (which is possible, but not very likely)
How should I have handle it ? Within my working time, I spent alot of time on the phone with a Mazda dealer telling them about the situation that no codes came out and that catalytic converters were clogged cause the repairman at the other garage saw them with his own eyes. But Mazda dealer kept telling me that he needs the codes even if they are clogged. Mazda dealer told me that without the code, it's on my expense, so do you think I should have taken the risk and fight them after ? What I hated the most and what I'm more furious about is the fact that they need the stupid code like proof !! It's like if they told me "Too bad if the computer didn't do his job, even if it's not you, we think you clogged them by yourself so too bad"
Any system can fail, but it is more likely that the shop that you took your car to lied to you about the codes, or simply didn't have the required equipment to read the codes. The warranty would have applied even without diagnostic codes, had you taken your car to the dealer. It is not hard to diagnose failed catalytic converters without an OBDII system.
If you damaged your cats by running leaded fuel, then your warranty would be voided. You voided the warranty yourself when you allowed the shop to repair your vehicle rather than taking it to the dealer.