B12 is practically standard for anyone ill with a bad gut. As electrolyte balance is also adversely affected by diarrhoea, you might need calcium, magnesium and the likes; obviously a physician's advice is needed there as just guessing could make things worse. On top of that, some Crohnies benefit from extra iron, although their iron levels do not appear to be low.
If you have an underactive thyroid, then I don't know how that would affect things in terms of absorption of vitamins, but you are very likely to have severe problems with fatigue same as B12 deficient people would.
I also don't get vitamins except from food, and on going onto B12 supplements recently noticed a big improvement in previously very severe memory and concentration problems, with a lesser improvement in energy levels.