i've always used a top box, with either soft or hard panniers - both have worked well for us, although personally I prefer the old Krauser K2 hard panniers to anything else. I've had 2 sets for almost 30 years and they've been faultless in use, although on our Fazer 1000 Liz has always used Oxford soft panniers (she has no issues with them whatsoever.
Although the Krausers have never leaked, we still pack things in plastic bags before we put them in the panniers, just like we do with soft panniers. Photo below shows Fazer with Oxfords and Givi Box and FJ1200 with full Krauser K2 set.