So the question is in the title... I know how the E, A and D strings tone changes after some time (as it gets rusted). But I don't really notice any difference with the nylon strings. So am thinking of buying only the E, A and D strings when I am planning on changing the strings.

So do nylon strings get dull overtime?

yes, they do. they also get dull in high humidity.
Quote by Skeet UK
I just looked in my Oxford English Dictionary and under "Acoustic Guitar", there was your Avatar and an email address!