As with any RV, careful maintenance generally prevents water leaks. Yes, the cabover portion is a weak spot on many/most class C's in terms of water intrusion.
I don't think there are enough significant advantages to either a class C or a class A to categorically prefer one or the other. Far more important IMHO is whether the design as a whole is suitable for your needs and wants. Very broadly and generally speaking, most class C's seem to be more geared towards families (lower cost, more sleeping arrangements, less opulence) while many class A's are more intended for (retired) couples.
I am very glad to have the driver's door on my class C. It makes fueling and especially maneuvering in tight areas without a spotter more convenient. It's a lot less hassle to get out and look when it doesn't require wandering through the house to get out. I also appreciate the idea of having another entrance or two should the hose door lock/latch mechanism ever fail.
On the other hand, a van chassis is certainly noisier and more cramped for driving than a diesel pusher, and it can get a bit warm having a V10 engine right underneath the dashboard and a foot from your right leg.