CrystalDiffract's Pattern > Label Peak Threshold submenu lets you specify a minimum percentage value, above which peaks will be labelled. Peaks whose heights fall below this value (which is relative to the maximum intensity in your structure) will not be plotted.
By suppressing labels for weaker reflexions, it is easier to "index" complex structures - and also makes for a tidier display, with fewer overlapping labels.
If you need more peaks labelled, simply select a smaller label peak threshold value, from the Label Peak Threshold submenu.
CrystalDiffract 6 includes a new Hide Overlapping Labels option which suppresses labels for weaker peaks if those labels happen to overlap a label for a stronger peak. This allows you to specify a lower (or zero) peak threshold, and let the program automatically handle label overlaps.