If you are a karate-ka, then you will want to work up to hitting the heavy bag with full force, speed and strength, w/o wraps or gloves. If you're a young person (younger than 15-16) then you might want to initially wrap your hands, until your knuckles, wrists and bones get use to the impact. If you do makiwara work you'll find that hitting the heavybag w/o gloves or wraps is actually really easy. If you have never hit something as solid as a heavybag, then work your way up to doing it full force. You can start by doing knuckle push-ups (first two knuckles only), adequate upper body stretching and light makiwara work. Use focus mitts and smaller striking pads first, start hitting the heavybag with control, not reckless abandon. This is why real MAs take years to master. Those that force the issue often wind-up being more damaging to the practititioner than any assumed foe could ever be.
If you are a yudansha level karate-ka, and you still use wraps/gloves and hit the bag only 1/2-3/4 force then you are not a real karate-ka. You are going through the motions, but a heavybag is really not a rough or hard surface for a properly trained BB, and so if you use hand protection then you are selling your art and training short. In the street every strike is full force, with bad intention(s) behind them. No set-ups or soft jabs, just crisp punches that go through the target, never overextend them. You need to condition your body for hard contact, bone-on-bone, and although this can be accomplished with koteate/kotekitai, kumite and such, you'll never be able to truly have the confidence or "iron body" needed to make karate really street effective. This is what's missing in many dojo nowadays.
If you are injuring your joints, then you need to increase your overall strength and flexibilty by stretching your whole body before and after doing bag work, and by lifting weights. If you do the traditional hojo undo of Okinawan karate, where you use earthen jars, chi-ishi and such then you are a step ahead of most modern karate-ka. If you don't have access to these tools of the trade weight lifting will definitely help your joints and bones, as well as ligaments and other connective tissue strength. You also need to use proper biomechanics. Keep your elbows in on linear punches and don't wing any of your punches, even the hooks. Strike using hip rotation (the body as a unit) and the power of rising and falling. Keep your fist vertical or better yet at a 3/4 turn (in between vertical and flat/horizontal). Do kata with focus and good structural "ki" and you'll increase sinew strength, too.
For your kicks, learn to whip them through the target in a relaxed manner, bringing your leg back quickly as soon as you penetrate the target. Get both legs back in your base as fast as possible. Balance is the key to movement and fighting. Doing that baseball bat MT kick as a novice will lead to personal injury. This is even true of the MT practitioners who do these haymaker, over extended strikes for a living. Many are crippled before 55 and that is the main reason you don't see 70 year old MT masters on the whole. You can practice push kicks and thrusts, but fast kicks are what will give you a chance to get the weapon there. The strength will come with time and increased speed.
One last thing. If you are working on a community bag, like a bag at the your local gym, using weight gloves or light wraps might be a good idea for infection control. You don't know who's been hitting it and if they bled on it, they may have Hepatitis or some other blood-borne disease. Although the chances are slim you'd contract the disease, it is better to be safe than sorry. Using an inch of wrap or padded bag gloves is for boxers and beginning karateka, not people who will need to hit without big cushions on their hands. Light wraps will be adequate protection from "bugs" and such.
Remember that the last 3 knuckles do not articulate (make contact with) the "wrist bones". Styles that teach hitting hard targets with the middle, ring and pinky finger knuckles are suspect. If their masters really understood the mechanics of delivering a hard and effective bare-knuckle punch, they would never teach the incorrect method (JKD and Wing Chun come to mind). The first two knuckles are in line with the bigger bone of your forearm (the radius) and they articulate with the wrist bones. For this reason contact with your target should be made primarily with these knuckles, the others taking a very minor load. I write this stuff to help out. Take it or leave it, but this where supplemental training differs amongst the various MAs and Combat Sports. Be careful of "Boxer's Fractures" and sprained wrists.
Peace and safe training...
