If they're clogged, the car would definitely bog down. It wouldn't miss like an ignition problem, just have no power and may sound strange. I've never heard of a cat 'clogging' though. My stock pre-cats went bad at 110k miles. The internal element actually became dislodged and was rattling around sideways inside the cat body which blocked the flow. Under normal driving you could barely tell. When I punched it, the car sounded funky like a WRX but went nowhere. I smashed both elements out of the precats with a crowbar which was a lot more fun than it should have been. No more problems after that and I still passed emissions.
Still, I'd do a tunup before dropping the H-pipe. You may need it anyway. Don't forget to clean the MAF. Do that first.