This is one of those instances where a manufacturer installed pickup system simply doesn't meet the needs of the player and an aftermarket would have been a better choice.
You need either an internal mic or a soundboard transducer to get the body hits. Different brands and different placement will give you different timbre of the hits. Many folk who play that style use two or even three separate sources. Thomas Leeb, for example, uses Dazzo soundboard transducers, an internal mic, and a soundhole magnetic pickup to get the full spectrum of sound from his guitars.
here is an example from Thomas played acoustically...
As for the type of guitar that will depend. Certain body styles are going to work better (generally small, the big dreadnoughts will be too boomy). Very important is the neck/action, especially if you plan to do a bunch of tapping (which often go hand in hand with that style). Player tend to use more "modern" (for lack of a better word) guitars (i.e. Lowden, Furch, Maton, etc.) over traditional brands such as Martin (although certain models may work very well). Probably best to aftermarket the pickup system so you can get the exact sound you want.
For reference, here is my friend playing his Furch guitar w/ SD Mag-Mic system. Is this the type of sound you are looking for?
Again, these are 2nd hand observations since I don't play this style.
One of the factors is to realize that the guitar is not going to respond the same way when you are amplified. So practice amplified and find out where the sweet spots are, for your particular system. If you think of it as a different instrument, you will be fine. Of course, you should explore other possibilities to see if they meet your needs.
Gabriela gets some of the fattest percussive sounds I've ever heard on a guitar (of Rodrigo and Gabriela, of course).