Bonus villages...
There are a number of things you can do with them.
If you get an academy, train noble(s), like all villages, you can capture them.
Or, as used by a lot of players, they are mostly farmed due to the bonus' they give. I.e. A 100% Iron bonus village produces Iron at a 100% faster rate (Twice as fast).
The Non-Resource/Warehouse bonus villages can be useful also, mainly by being Captured, but also sometimes waiting for smaller players to get them, and build them up for you, to make a better target.
The "Best" bonus village (Imo) is the 10% Farm Bonus, as it allows you to build an "Oversized" nuke.
The bonuses they show are in effect constantly, whether being Captured or not. The only ones that will effect uncaptured bonus villages (on the outside, it will still happen internally) are the Resource/Warehouse ones.
In summary, they can be nobled, but not many good players tend to noble them first off. Late game, they can be of help though.
Hope it helped
YGP <3