What is meant by dark notes in jazz could it be the lower register?

If you post a link to this intro I could give you a better answer. Hope this helps, tho

In short, Yes. It's common to refer to the timbre of a note as "dark," although its very subjective; i.e. there's no definition that makes a note "officially" dark, it's just something people say to describe what they hear. In fact, there's a certain range of the clarinet that's actually referred to as the "chocolate" register:

http://www.wksu.org/classical/2009/06/05/clarineti...

It might also be a reference to the mood of a particular passage

You sure he didn't say "blue" notes? The "blue" note is the sharped 4th or flatted 5th in a blues scale. It can be used elsewhere too, but that's where the name comes from. For example a C blues scale is

C Eb F F#/Gb Bb

in this scale, F# (same as Gb) is the "blue" note

Sharps & Flats