The spells do not interact
Darkness doesn't make creatures invisible; it makes it so creatures can't see well in its area. (It's not even total darkness in 3.5, just "shadowy illumination"):
This spell causes an object to radiate shadowy illumination out to a 20-foot radius. All creatures in the area gain concealment (20% miss chance). Even creatures that can normally see in such conditions (such as with darkvision or low-light vision) have the miss chance in an area shrouded in magical darkness.
Note that invisibility gives total concealment (50%), so this is less than that.
Even if it made them "effectively invisible" by plunging the area in total darkness (as in this case, because it negates the prevailing light sources), it still doesn't make them actually invisible. Creatures are harder to spot because people in the Darkness can't see as well, not because the creatures themselves are intrinsically harder to spot.
Glitterdust, then, won't have any special effects. It will make actually invisible creatures potentially visible by giving them an outline (but still not actually visible as they are in total darkness), and it potentially blinds the targets. Non-invisible enemies are outlined as normal, but that has no mechanical effect, as normal.