You can get larger knuckles and the Bone Density can be increased. I've written before about the topic in great detail, and seriously recommended people with fragile hands to slowly work up the power by doing barehanded punchwork on a 10-15lb sand bag. Get 2 potato sacks one inside the other and fill the contents with sand so that its roughly the size of a human head. Tie up the top tight so that it has the dimensions of a regular speed bag or slip bag. It is absolutely the most useful piece of training that I still keep since my Kungfu days.
If you start off with this small but dense bag, you are very likely to get wrist collapse, bruising on the fist, or most commonly, tearing of the skin. But nevermind it, your intentions when starting off is to hit this thing lightly for the first three months, just rap it everyday with the back of the hand (like youre doing a speedbag workout), the fingers, hammer it with the palms, give it a few punches with the knuckles -get a total conditioning all over the fist in every direction, if you want to toughen the wrist, then use backhands on it.
Every month you should increase the power, just a little slightly, remember that increasing the bone mass is a slow process cause it takes a while for the body to trigger what is known as Osteogenosis, an effect in your body which causes your bone mass to increase in weight and density. The more dense the bones are, the less likely you are to get fractured bones. The harder your bones become, the harder you also hit.
Constant hitting with barehand also thickens the nerves, the thickness of the bloodvessels inside the hand and the intercostal muscles between the bone fragments in the hand going all the way up to the forearms, most importantly you'll start building a good callus if you ever need to get into a street fight. If you take a look at laborers they have huge hands, it didn't get there by accident and they aren't born like that; they do so much rugged work with their hands daily that the bones are much larger and heavier than ordinary people.
Barehand hitting emulates that stress on the hand, and if you ask any Hard-Karat guy especially a breaker who can crackshit through watermelons, blocks of wood or bricks, they all go the barehand path -wood chips -> Sand -> Steel filament for their bag filling in that order.
Real breakers are not gimmicks and nor do they cheat. If you've seen photos of the old Karate MAsters they had hands like alligator skins, with pronounced knuckles and concentrations of callus around the top two knuckles, that shit is so hard if it hit someone it would probably kill, if not at least break bones in an instant. The entire fist is fused with the forearm because of the immense strength in their wrists.
Anyway here's my old Kungfu workout to get my 'ugly' hands:
-Finger pushup
-Knuckle pushup
-pushups on the top of the wrists (you should do more of these)
-Barehand striking
If you cant do a finger pushup yet, Get a bucket of sand, and stab your fingers straight down into it. The fingers will eventually get real hard (They also get shorter for some reason), and you can poke someone's eyeball out if you ever need to.