Well when not in use a waterproof cap it essential as water filling your socket up is going to play havoc with connection corrosion, if it stands outside like mine most of the time (and when travelling) keeping water out is a good idea, when in use with most bikes the fairing and screen tends to keep the majority of water out of the socket, its when you stop or are in traffic and its hurling it down that water can get in. Most charger leads just have the power supply leads connected, but most leads that come with your phone or PDA have data connection leads also which its why not a good idea to have water ingressing into the plug and socket.

For a modest outlay you have peace of mind in that the connections are dry and corrosion free, with cigerette connectors and din the connectors are way apart so water ingress is not a problem but usb pins are small, prone to damage and tracking as the connections are so close together. The integral usb sockets offer a compact solution whereas  din and cigerette sockets are bulky and can foul the handlebars when you have a convertor plugged in, plus the cigerette type convertors invariably self distruct with vibration.

The battery could be immersed in water with no effect as the terminals are far apart for water to short it at 12v as to the din and cigerette versions, but smaller connectors like on the Versys are sealed with a rubber seal in the plug, particularly on electronic devices like ecu and associated injection components where the currents are small and close  together then water can short the electronics.

Besides the corrosion problem unpure water contains ions that readily conducts over short distances and causes electrolysis (absolute pure water does not), the higher the voltage the easier it conducts, at 5v the effect is tiny but still present which causes corrosion and can upset sensitive electronics. As I said with charger leads that just connect positive and negative then possibly no problem, however a combined charger/data lead can wreck your PDA or iphone or smart phone etc if water conducts small curents in the wrong place.