Ondansetron can even be given four times a day if needed, but I've usually been fine with twice a day dosing, except if quite sick. You can always try lowering the number of times you dose, but you do want to stay ahead of nausea, so it's tricky. If you lower too fast he might get nauseous again.
I see you are giving just 2 mg per dose? For his size, he could easily do a 4 mg pill. He might be under dosed. My 8 lbs cat gets 2 mg and that's the low end for her. Dosing for the oral drug is 0.5-1.0 mg/kg of cat every 6-8 hours. 16lbs is 7.2 kg so he could get 4-8 mg.
Some cats need time to get used to meds. With Neko, it took her 2-3 days before her body got used to new meds, often with higher numbers.
Many cats with IBD or SCL have pancreatitis episodes. Unfortunately you can't use blood work to diagnose IBD or SCL.