There are problems both ways.
With text dueling there's the trust factor.
You have to type up everything and keep track of everything manually.
With YVD there's the connection and compatibility factor.
Some computers don't support IRC or any other programs YVD might need to run properly.
There's also the connection factor. Sometimes your internet might disconnect, and you'll be forced to reconnect your YVD and start your duel over again. Now, if you're winning, won't that just be a b***h? I'd rather be able to resume as I reconnect the internet, than be forced to start over.
Then there's always the glitchyness of YVD. YVD is a fan-made program, much unlike YGO! Online, and tends to be very glitchy. Among these glitches include cards disappearing all of a sudden, the program itself crashing, and many more which I've experienced firsthand.
This is why I'd rather text duel. Sure, your opponent can cheat, but I know I'm not. It keeps things simple.