Crohn's in the small intestine can be very difficult to find at times. After all, we have some 20 feet of small intestine and its all looped around in the abdomen and very mobile. The only value of a colonoscopy for Crohn's is if the Crohn's is active in the colon or very near the ileocecal valve and very end of the terminal ileum. The colonoscope can't reach that far past the ICV and sometimes the doctors can't get the scope thru the ICV even if a healthy colon and small intestine.
Probably the most effective way to find Crohn's in the small intestine is the Pill Camera Endoscopy and if one is strongly suggestive of having a partial or full obstruction there is a risk of the PCE getting stuck and requiring surgery. Anyone considering a PCE with reason to believe they have a high grade partial obstruction is to insist on the use of the Agile Patency Capsule first. This is a capsule that is the same size as the PCE capsule. But the APC will dissolve w/in 3-4 days (or is it 2-3 days? I've forgotten). You swallow the APC and 24-26 hours later you have an abdominal xray to see if the APC has passed or is stuck somewhere in the small intestine. If it has passed you are a good candidate for the PCE.
The problem w/the PCE is that it is not the most cost-effective way to discover Crohn's disease so many insurances are reluctant to pay for it. The only reason the colonoscopy has been the "gold standard" for Dx'ing Crohn's is because 1] if there is any colon involvement and 2] the most common area for Crohn's to strike is at or very near the ICV and of course, 3] biopsies can be taken during a colonoscopy.
And you're right, once you've been Dx'd w/Crohn's, even when not encountering any symptoms you should remain on maintenance meds to help prolong any remission.