Hiding behind walls is actually a bad idea when facing melee units like buccaneers or Native Americans. First, the firepower of your units is lessened. Only the front row seems to fire. Some have said fire by ranks makes this better but it seems silly that I have to research that to get a decent RoF from my guys.

Second, cover doesn't really hinder charges much. In my experience, at least. If given a running start, units can jump straight over cover, right into your unit. This should result in a bayonet sandwich but it doesn't. Cavalry barely seem hindered in the initial charge. Once stopped, their horses can have issues getting over the walls but the impact is still quite hard. Infantry, who aren't as wall challenged, are worse.

So, you end up killing fewer enemies at range and then having little to no advantage in the ensuing melee. Since melee units can't shoot back, I'd rather just deploy my men normally, in longer lines, behind the walls. That way, they can give off one nasty volley before they have to melee and maybe some enemies get tangled up on the walls. The PITA is when you face the sometimes charge-happy light and line infantry. Never know if the AI will want to shoot it out, where cover is quite awesome, or charge, where cover doesn't help as much. Though I haven't tested them as extensively, all this also seems to apply to the deployable "trenches," which are really walls.

Now I, the player, would never charge my men in such a manner, it's a pointless waste of lives. There are better ways to assault such units. The AI, usually having plenty of men to waste and the tactical brilliance of Larry the Cable Guy, doesn't care. It seems strange that it works so well anyway.