In your 12 week transformation workout for building muscle you sometimes recommend 30 reps for exercises that target abs or the oblique’s. 

Why is that? Why do these muscle require so many repetitions? Combined with short rest periods (30 seconds) I feel like my gains are being held back by lack of breath (I know I should exercise more cardio).

I have also noticed that other exercises that come last in your programs also often have high number of reps. I find this though because I'm often exhausted by the time I reach these exercises and feel like the high number of reps is holding me back here as well.

Just because you are out of breath, doesn't mean you are missing out on gains my friend. Muscles grow when they are taxed and put under enough stress that they breakdown, and then HAVE to grow back bigger and stronger. For abs, I personally like to do a mix of both high rep and heavy weight training. Bodyweight ab exercises I go for higher reps, because your abs can take a beating and simply don't need as long to recover as other muscles - that's why you can also hit them pretty much everyday without any negative effects. It's just the way they are - think about it, they work a lot to keep you upright when you're standing etc.

And for the exercises that have high reps at the end - that's the point of having them there, they're finisher movements. You should have already smashed the muscle group/s by the time you get to that final exercise, so it's not about lifting as much weight as possible, it's about putting it under stress to make sure it is definitely broken down so it can grow back bigger and stronger :-)

Make sense?