Archers do not require Line of Sight to shoot, but suffer penalty from lack of it. Gunner units do require Line of Sight, that means their missiles can't fly over tiles that are above themselves, so Crossbowmen can't shoot at people over a hill that lies between them, but can shoot at, for example, ones standing on a cliff over sea.

Now where it gets difficult is that certain terrain features (woodlands, forest) and even your own units are considered an obstacle and to shoot above them you need to be two levels of elevation above. Also, unlike usually in hex-based strategies, the missile needs all tiles to be clear to fire above them - for example if the missile would fly over two tiles side by side, generally only one of them would need to provide LoS, in HK it's both.

If it's still confusing, the game helps by highlighting the tiles with enemy which is a possible target with red border when you choose where to move.

Something else counterintuitive, and often irritating: The obstruction doesn't have to be fully in the way. If your gunner unit's line of sight is merely half blocked by an obstacle (no matter whether that's another unit, fortifications, mountain, etc.), it can't shoot the target.

In addition, I often have trouble shooting across water, especially from one region to another.