Connectors, if not waterproof, will be the largest problem. Good waterproof connectors, properly installed, will help prevent connection issues between the controller and the rest of the bike, even if exposed to the environment. Which connectors you need depend on what signals you have, and the power levels you have to deal with.
The entrance of the wires into the controller, and the controller itself, if the controller is not potted, can be a problem. If all the wires enter the controller from one end, putting that end on the bottom may allow any water intrusion to exit without contacting anything inside the controller, as long as there is sufficient space between that point and the stuff inside to contain any water and there isnt' any splashing inside from vibration, bumps, etc. Having them on the top like in that picture means that any water that does get in thru the wire grommets is likely to accumulate inside and damage the internals.
Sometimes, with "sealed" devices (which are rarely actually sealed fully, as in IP67 or better) that don't fully keep out water, but are never actually being submerged, it is helpful to add a tiny drain hole at the lowest point to let out whatever does get in there. It depends on your specific weather/etc conditions, and usage.
If the controller has any bolt-on connections on the outside (phase, battery, etc), or exposed connector junctions at the body, you can try using dielectric grease on the connections, inside the connectors, and outside them, to help minimize water intrusion.
Wires themselves, if insulation is intact, are generally ok with environmental exposure, though sunlight (UV) will degrade the insulation over time, so a "jacket" around them is helpful for that.
The jacket, if tough enough, can also provide some measure of protection against impact and abrasion on the wires. If a lot of this is expected, I'd recommend a hard casing around the wiring and connectors to prevent damage.
