I'm starting to think getting smashed into the ground on a regular basis might not be too good for the body.
This is actually a very valid question. Consider that the NFL (U.S. football) is now going through a kind of falling out period whereby the athletes are becoming more and more aware of the growing risk of chronic brain injury over time. In the UFC, we're starting to see some questions regarding brain injury rates as well. And for a long time, we've known that boxing can really damage the brain.
In Judo, practitioners will constantly throw each other to the ground where they make a sudden slap and a thud. Whenever I entered judo training after a long hiatus, I would notice myself getting headaches. It only lasted the first day or two back, though. The sudden jostling around of the brain could cause injury over time, but I'm not sure that there is any data to support that hypothesis.
My gut feeling is that the forces on the brain during a judo breakfall are minor compared to that of getting punched in the head (something judo doesn't do). Judo breakfalls do slow the head motion while falling down so as to cushion the landing. It does so by using the neck muscles to gradually absorb the momentum of falling, so that the head doesn't just suddenly hit the ground.
But I have no idea what the forces are and whether they would affect brain physiology in the long-term.
In addition to breakfalls, there are chokes in Judo. Chokes work by applying a force against the arteries in the neck. This can be slow or sudden and sharp. The effect is to cut off the blood supply to the brain. It can also trigger a nervous system reflex to suddenly drop blood pressure, thereby instantly causing someone to pass out. Both will restrict blood flow to the brain. In addition, they can have an effect on the heart. And, in rare cases, they could dislodge arterial plaque into the bloodstream, causing a stroke.
Obviously, chokes could have some effect on long-term health.
Then there are back injuries, neck injuries, shoulder injuries, knee problems, hip problems, sprains and strains, and so on.
One interesting thing to point out is that there is very active self-policing going on in judo itself. The International Judo Federation (IJF) has banned many popular judo throws due to safety concerns. They get together once a year to look over injury rates during competition for all of the throws, and when they notice a particular throw causing more serious injuries than other ones, they might ban it.
EDIT: Dave Liepmann pointed out that morote-gari is not a good example of this. It was not actually banned for safety reasons. However, Kani Basami was banned due to the higher risk of knee injuries.
You can actually see a video showing the entire list of IJF banned throws (from 2010) here: https://www.youtube.com/watch?v=XhOmAyjTimc
So, bottom line is that Judo as a whole is very concerned about injuries. When I trained in Judo, our school didn't have a "macho" attitude about things (and I've never seen a macho attitude at any judo school I've visited). Safety was always the top concern.
Anyway, I post this to clarify the main question, rather than answering it directly. I don't know of any long-term health studies. Those are what you really want. If anyone has them, post them.
Consequences of doing judo long-term:
And hopefully, maybe, if you work at it, one might be able to cultivate some jita kyoei and seirokyu zenyo.
Anecdotally, Judo can be absolutely brutal on your body:
Going beyond mere anecdotes gives us better quality information.
A few key points from http://www.ncbi.nlm.nih.gov/pubmed/9487650 where 8 Judo practitioners were followed for 16 years, and their fingers were examined:
http://judoinfo.com/research11.htm has a study on competition injuries for the young.
A wise quote from an anime...
You can mitigate risk. Here are some tips, I hope they help, and I hope you don't have to learn things the hard way:
Be Sensible and Self Select,
Everybody is different. Some people are flexible, some people are born with the genes for good cardio. Everybody has different motivations. Judo is a choice. Does it make sense for you?
When looking at the statistics for injuries, remember that some people will drop out of Judo because they should. If you discover your body is the type to be extremely likely to be badly injured from an activity like Judo, then it wouldn't make sense to do it.
I think you can answer two-way to your questions.
1st, long term risk to your body depends on how you train. If you have bad habits, and you apply useless strain on your body, it WILL catch up to you (at 40 some morning I feel like I have the knees and the back of a 60's). But its also part my fault. My mom ( who was also my 1st coach) always told me to take care and not land on my knees after finishing some throws ... but well I was young and enthusiasm lead to excess.
2nd would be injuries. Those will happens in any sports where you train extensively and cant be prevented, accident do happens. Those are more specifics to each person.
as for judo specifics injuries, I'd say back problem, most major articulation (ankle, knees, elbows ) problem and fingers ( huge strain are placed on fingers, and people often forget to exercises them correctly) are the most common. I've never seen/heard a judoka with chronic headache or concussion related problem yet.