It is true that the FNA can generally only be done if there is suspicious tissue to be aspirated. But, endoscopic biopsies can be just as easily ineffective, as they do not always collect the correct tissue. There have been numerous posts on this site to that effect. Not only that, endoscopic biopsies are considered invasive (albeit 'minimally'), are limited to the proximal gastrointestinal tract (meaning they will not normally include the colon - that is a separate procedure called a colonoscopy biopsy), require anesthesia, and usually mean some recovery/down time. I am not suggesting NOT to do an endoscopy, but the OP needs to know the differences and weigh the risks/odds.You can have an endoscopic biopsy done--- not a Fine Needle aspiration (FNA). The FNA would have to be targeted to one spot. The endoscopic one can see if there are many areas of suspected IBD in the stomach. Yes, thickened walls of the intestine is a sign of IBD and/or SCL.
I will point out that steroids can also skew the results of an FNA too.
The thing about all of this is that treatment usually ends up just about the same one way or the other - dietary changes, various meds to help control the effects of IBD, steroids, and chemo if steroids don't make enough of a difference. Some forge ahead administering chemo concurrently with the steroids, just because the type given to cats are usually tolerated well. Of course, this - like anything else - depends on each individual cat.