He may be more presence than flesh, but he still has a physical form. And if he has been sitting pretty with the Dark Side raging inside of him for 5,000 years (or whatever) then that has to do something to him... Whether it be weakened attributes, insanity, you name it.
As for the makers of KOTOR 2... I think they may have gone a little overboard with the new ideas they obviously want to push out. I mean, they make the whole idea behing Nihilius quite frustrating to understand to begin with, and then they don't even fully explain his situation or what he is.
From what I gather, Nihilius sounds like he's passing into becoming a Force Spirit, from the quote you offered just before.
Sure they have a few lines here and there about him, but nothing explaining everything completely. Seems to me they've taken the easy route and just said: "Yeah, the dark side planet did it to him." Which leaves me wondering how exactly a planet can change a person in such a way simply through essence being passed on? Surely there's more to it than that.
I personally think you should keep the idea of Nihilius, but alter him enough to make him your own. In the sense of giving him limited abilities which aren't too powerful, which so far most of the ideas you have are... They are much to strong, quite honestly, at least for RP purposes.