Dual wielding monk weapon? Yes, its very good with at least 1 monk level and there are many powerful ones at all level ranges.

Specialize in nunchucks only? No, however, there is a flaming one very early in a very hard location for lvl 3 call Tranquil river bend. A little bit south of Temple of the Elk chap 1. The nunchucks are on a corpse at the entrance of that zone.. loot and leave or have a very hard time in that area at level 3. Easier at lvl5 but still hard

Ya, I just picked those weapons up playing around and that is what spawned this thought, I know they work with Flurry of Blows, so you using one of them would be fine, wasn't sure though if TWF was feasible with them or not, or if you'd just use the one and have FoBs for alot of attacks. I wanted something along the lines of InEffects Dueling Monk build but instead of Kamas, using said nunchucks.

Anything is possible. If it's gonna be good - that's a whole other question. Not in the least cause I don't recall any half-decent nunchaks past A1. Shouldn't be a problem for challenging, though. Nothing is.

Well, one of the main Monk's "powers" with extra levels is "unarmed" bonuses - extra fist damage, etc. If you want to use "monk weapons", just get 1 level in monk (gaining AC bonus and Flutty of Blows), then invest other levels into another class. Cleric is one of the best choices. Actually, Cleric(Eclessitheurge) with 1 level in monk(Traditional) is probably the STRONGEST build ever. He can best a whole game solo (except for last boss).
You can also choose Sorcerer, if you want, or even a Paladin.
Also, i'd recommend to not focus on specific weapons for that build. Weapon-specific traits are trash for it anyways. So it's better to skip them and use whatever best weapon you find. Oh, and you can use non-monk weapons in offhand too (it doesnt prevent an effect of Flurry of Blows).
BTW, the main problem with Nunchackas is that there are NO decent unique nunchackas in the game, so finding a good nunchacka is a roulette (there is a chance that RNG grants you a good one, but it's foolish to rely on it).
And among all monk-specific weapons Sai is the best for DW. Why? Because there is a unique sai with "Greater speed" mod, granting you +2 extra attacks per turn.