I've always been a one or two pannier guy. Depending on what I need to bring. I have been fortunate and only needed to schlep a netbook for a couple of months.

I just put out in its neoprene sleeve and went. No issues.

In 10,000+km I have only lost a pannier once. That was on a new route with a bridge and bad expansion joint at 25 km/h. The expansion joint has since been improved.

I have recently started using a top tube pannier. I put my keys, phone, wallet or money clip and my battery pack for my light. I only secure it with one Velcro and pop my lights off and into it and bring it inside with me. Easy peasy, my man biker purse. I add snacks as needed. Only if I stuff it with everything two sandwiches and an apple have I had problems hitting it with my leg.

My panniers aren't waterproof but I just lined them with my unused kayaking dry bags and then load them up.

Edit. My pannier is one open hole, no divisions and I prefer it like that. I have one outside pocket which I put my tools in. Two mesh pockets I put my pump and lock in. Top pocket on the outside for hat in the cold. Top inside pocket for map, emergency bus fare, minimal first aid supplies and a candle and matches and knife.