Black thread on black fabric is very difficult to see when machine quilting. As you are hand quilting you shouldn't be concerned. If you want to use black thread go ahead. If you want the quilting to pop a bit use a dark color thread, maybe pull one of the other colors in your quilt out. I have found that dark purple, navy blue and forest green blend well with black but offer just a wee bit of contrast so you notice the quilting more than if it is black. If you want the quilting to pop use a high contrast thread which could really compliment your applique without overpowering it.
A 30 wt hand quilting thread really doesn't show up a whole lot and certainly won't compete with the applique. Here is a link to a quilt I hand quilted with a yellow variegated 30 wt thread (Valdani brand) on almost black fabric. You don't really see the quilting until you are close up.
Hand quilted Mariners Compass WIP