Well, if you're wearing leather or chain armor, a good blow from a nunchaku is still going to cause a heavy bruise--even splint wouldn't be able to shrug it off completely. Whereas, if you're up against somebody armed with a whip, all you have to do is wear a half-decent cloak and make sure to protect your head, and you're invulnerable.
I do hear you, whips would make a very nice roleplaying addition--I just don't think they're that feasible. I mean, I'd like to introduce an enemy whose favored weapon is a short-handled spear with an envenomed whip at the butt end, I simply realize that it ain't gonna happen. As far as I know, BG2 (and therefore Tutu) still has BG1's proficiencies of Blunt, Large Sword, Spiked, etc., still lying around unused, and you could theoretically hijack those (or at least one of them, and rename it "Exotic"), but I don't believe you'd ever be able to increment that proficiency at Character Creation or Level Up--meaning the best you could do is have a recruitable NPC who specializes in exotic weapons, and give them a script to increment the Exotic proficiency at certain levels.
Failing that, all you could do is slap Whips into the Flail proficiency. As I've said, Whips are almost entirely unlike Flails, but at least that makes more sense than, say, Halberd.
Personally, I kind of like Tamoko as a Cleric. Making her an Assassin or Kensai goes against the grain of her dialogues, which are very pacifist--but Dragon magazine wants her to be Ninja. Either way, she's supposed to do a single hitpoint of damage to CHARNAME in the first cutscene, and I feel that a Cleric could accomplish that the easiest--just turn the (nerfed) Flame Arrow into a Magic Stone and there you go. As for a Kara-Turan Cleric wielding a Katana, I would have no problem with that at all.