In the general sense, everything you change affects the resonance abilities of your instrument. I'm not sure you mean neck so much as fretboard in this particular case though?
but seriously, there are way more pressing issues than fingerboard wood. some folks say maple sounds brighter than rosewood. it certainly LOOKS brighter, but i can find no evidence that it makes even a tiny bit of difference with the tone. and even if it did, a turn of a treble knob one way or the other could completely nullify it. so who cares? get what you think looks cool.
Some say it does. Some say it doesn't. Do you perceive a difference? And, I think you're talking about fretboard wood here, not necks.
IME, yes different necks sound different. I know this because I've changed lots of necks and listen really good. However, you're going to have to have a congressional commitee appoint a blue ribbon panel of the world's megageeks to convene a convention to produce a peer reviewed paper to prove whatever it is you may say on TB.
A maple neck with rosewood fretboard and rosewood neck with rosewood fretboard, The all rosewood neck would be little bit darker and woodier tone then the maple neck with rosewood fretboard. Though I'm not sure is rosewood is that good a choice strength wise for neck itself. Ovangkol might be better choice as alternate to maple for woodier sound and little less treble. For fretboard I think maple sounds less organic somehow then rosewood. Little darker tone to rosewood as well. But for just fretboard itself, theres not as much diff when compared to the neck itself or whole neck.