Octobergirl, I cannot think of why Crohn's would affect your ovarian or pituitary function. If you are malnourished from Crohn's, then perhaps that would be why.
On the other hand, I do believe that the hormonal cycles a normally ovulatory woman goes through wreaks havoc with bowel disorders. It is a good thing (from the point of view of minimizing your bowel discomfort, joint pain, etc.) that you are not cycling. Maybe that's what your rheumy meant by saying you should stay off hormones (like BCPs) until you have achieved remission.
Pregnancies with autoimmune diseases can go one of three ways. Your autoimmune disease can get worse, it can get better, or it can be the same. There is an equal distribution of these responses to pregnancies among people with autoimmune diseases (like asthma, arthritis, crohn's, etc.). For me, my asthma got much, much worse. But my bowel disorder got much better. Probably because I no longer had weekly changes in my hormonal status, just a constant dose of estrogen, progesterone, etc.
There are a myriad of reasons why some women don't menstruate regularly. If you are serious about getting pregnant soon, you should see a reproductive endocrinologist and explain everything you're going through. A regular OB/gyn who doesn't pursue amenhorrea in a young woman should be left in the dust, IMO.