My kiddo has always had biopsies done, even when her scopes looked great. She actually did have a couple scopes where the intestine appeared visually healthy but biopsies showed inflammation. We were told by her adult GI that they don't do quite as many biopsies as her pediatric GI did, but they always do them.
If his terminal ileum has been the problem area in the past, I'm surprised they would not biopsy there...the terminal ileum is my daughter's problem area too, although she has had active inflammation all through her colon too, and so her GI has always taken more biopsies there.