I have used waterproof panniers a good bit and had absolutely zero problems with moisture in the bags. I do take some precautions though. My tent never went in the panniers so even if it was wet moisture from it would never contaminate the bags. I took care to either leave damp stuff out or segregate it in a plastic bag. I have not found it hard to keep things dry when packing or removing items with a little care and planning. Just put the things you will need next where they are easy to get to.

I think the bigger issue is not waterproof vs non waterproof, but rather number of compartments. Stuff can be kept dry easy enough either way.

As far as lots of compartments... I see more disadvantages than advantages. I much prefer to organize gear, food, and clothing in stuff sacks or ziploc bags within a larger single compartment. I find it easier to pack all my stuff in a given number of liters that way and also find it as easy or easier to find things once they are packed. Ever notice how lost things seem to be in the last compartment you open? That means the more compartments the more places to look when you forget where something is.

I have used non-waterproof panniers with pockets and they were OK, but the waterproofs definitely worked out better for me.

I started using dry bags instead of panniers in recent years with the same excellent results.