When I was hired in my final "real office job" they knew I was also trying to have a baby. Since nothing comes easily for me, pregnancy was a difficult thing. Once I hit the three-month mark, I told my employer. I know, this is a "short term" thing, but there is a point to all of this. My pregnancy went bad, fast. I wound up working from home and also going on short term, that went into long term disability -due to complicating issues. I was glad I did it the way I did because I needed to use up sick time and vacation time before I could get paid for my short term and subsequently long term disability. It helped my employer know what was going on, because he knew to keep a temp waiting in the wings. As an employee, I think you owe it to your employer to keep them informed and to help them prepare in the event of a necessary long absence.
After I went back to work, I had to hire an assistant. Nice enough person, very competent, but she was out, A LOT! It was hard dealing with that, at times and finally, I needed to have a conversation with her about her large amount of days out. After about 15 minutes, she finally told me that she had lupus and was in an active cycle. It all made sense after she told me. Some days she was just slower and seemed so fatigued, other days she was quick and never had to be reminded of a thing! She was a good worker, but the days when she was so fatigued, it was frustrating. After she told me, though, it made sense and we worked out a plan. She was able to work from home on some of her work on the days when she was struggling too much to be able to come in. The other days, she ran circles around me.
Because of our company's policy, I did have to put something in her file about her large amount of absences, but after she told me, we never had another issue - we worked together. I wish she would have told me to begin with, because I could have avoided having to discuss her attendance.
It's against the law for an employer to discriminate. I know that even though it is, they can find ways around the law; however, I (as an employee) would still lean more to the side of disclosing an illness or condition to my employer. I can look back and see how it helped my employer to know what was going on with me and it would have saved some stress in dealing with my assistant.
As far as affecting your long term disability through an employer, no it shouldn't. You need to understand the policy: do you need to use up all your sick time, personal time and vacation time? do you need to go without pay for any length of time? how do you document your absence? can you appeal if denied by your physician or the insurance company?
Keeping your employer informed should help a situation; however, if you feel that you are being discriminated against, in any way, you need to see your HR Department about your concerns. If it isn't resolved, you should seek outside help.