Homogeneous and complex nuclei
I think you are reading too much into that statement. The proper reading of that statement is to add on the implied "..compared to other nuclei." That is, what defines a nucleus, in most cases, is some shared similarity in connectivity. That does not mean homogeneity.


I also think your reading of the second statement is incorrect; it does not suggest that there are "simple and complex" nuclei as two distinct categories, rather it is indicating that "complexity" varies, and gives a couple examples; essentially, it is exactly saying that you should not assume homogeneity. 


I don't think it makes much sense to think in terms of "number" of nuclei, and anyways, nuclei can be somewhat arbitrary. For example, take the auditory thalamus: the medial geniculate nucleus (MGN). The MGN is typically divided into three parts: the dorsal, ventral, and medial divisions. Someone chose to call them all the medial geniculate nucleus, based on gross appearance, but with more functional understanding we can classify each part separately. Should this be one nucleus or three? It really doesn't matter, it's just semantics and terminology to get people talking about the same structure. In one context, it makes sense to talk about the whole MGN, in other cases it makes sense to differentiate between MGv, MGm, and MGd. You could call them subnuclei, or nuclei, or whatever you want. Most people choose to just be consistent with the terminology used in their field for historical reasons because it doesn't matter.
I don't really think it makes sense to think of in terms of prototypes; nuclei are different from each other.
Again, you'd have to first define simple and complex. I don't think there is meaningful dichotomous distinction.