Hi, Koala,
I have Crohn's disease, and I have been very open about it on my apps. I even wrote a little about it in my personal statement, as it was one of the factors that led me into medicine. It was only brought up during one of my interviews and not in a negative way, just they just wanted to know how I cope when I am sick (and, for what it's worth, I was accepted to this school, so they didn't use it against me). For my so-so numbers, I think I have had pretty good success so far -- five interviews. Of the three that I attended, I have been accepted to two so far. I don't think it hurt me at all to disclose this information.
For your question about coping with it while being a doctor, that is something that worried me a lot, too, when I was first diagnosed. The best advice that I have for you is that you should work with your doctor to find a maintenance plan that works for you. You might not figure it out right away (it took me about a year to get my disease under control), but you will. Once you get your disease well-managed, things will be a lot easier and feel more "normal." And, yes, there is always that uncertainty of whether you may get sick during medical school, residency or practice, but I think that the strategy is to have a plan to deal with the difficult days and just keep living your life. That's all you can do. None of us know what the future will hold, so I don't think you should base your decisions on whether you might be sick tomorrow. There are so many things that might happen tomorrow that are out of you control, so the sooner you learn to "roll with the punches," the better. At least, that has been my experience and that of my friends with chronic illnesses.
If you have other questions or want to talk about it some more in private, feel free to PM me. I'd be happy to share my experiences with you or give you advice on your situation.
Good luck!