A couple points...
First Ortleib isn't the only choice for waterproof panniers.

Second the notion that long tours somehow make waterproof panniers a bad idea is nonsense. On my first tour we went coast to coast on the Trans America and between the three of us we had 10 waterproof panniers and two non waterproof ones. They all worked OK. We had absolutely no issues with either. My companions on the TA each wanted to have one pannier with pockets so they each used two rear and one front waterproof panniers with one non-waterproof pannier. I will note that when one of my TA companions subsequently went on half of the SC route with me she opted to go all waterproof when she had the choice of either available.

I have done a bunch of other 1000+ mile tours including another coast to coast trip and never regretted using waterproof baggage or had a moments problem with them.

Either type can work fine though. As I said the preference for pockets or one big compartment is probably the bigger factor in choosing. If weight is important to you (it is for me), non waterproof panniers with pockets are usually a good bit heavier even before you add a cover. For me one big pocket is much more convenient and being waterproof is a plus.