In the WSC, the thief/ninja is totally worthless.

I played a party with a fighter, theif, BB, and RM in order to compare them.

Fighter: best all around before and after class change. Always does great damage, always has best armor, has highest hps until rather high levels (30+).

Thief: worthless. Can't run better than anyone else (unlike in the NES version). Attack damage far worse than the RM, worse armor until you get bracelets, and no magic. When he becomes a ninja, he gets slightly better armor than a RW, but his hps are about the same as RW, and he does about the same damage. Only the RW has more spells, more useful spells, and wasn't absolutely worthless for 15 levels or so. There is no reason to take a thief over a RM.

Blackbelt: worthless before level 10. RM has better damage and better armor. After level 10 he finally starts doing decent damage. However, he never really surpasses the fighter at anything until level 30+. His average damage is no better than a fighter, his high hps are worthless as he takes gobs of damage from every hit and drinks oceans of tonics, and he looks silly. There is no real reason to take a BB over a fighter. Note I say average damage...he is capable of occasionally getting a lot of damage in one attack because he attacks a lot, but he rarely gets all his hits in. So while he can do more damage than the fighter, he also often does less, and it's more or less even on average until you get to really high levels...far more than needed to beat the game.

Red Wizard: nice class. In early levels (up to about level 15), has as many spells as WM and BM (fewer higher level spells, but you rarely use level 4 spells at that point anyways), and has better hps, armor, and attack damage. Fights better than the theif, as good as the ninja, and about 1/2 as good as a fighter or BB. And early on he has pretty good armor, making him tougher in those tedious early levels when the BB and theif are totally worthless and getting mauled.

So that's it really. Figher > BB, and RM > thief. No doubt about it.