What you have written is all essentially correct. I'm not sure whether the Voiceless Ones were actually intended to be mind-flayers in the D&D 3.0 version of Arcanis, but if I remember correctly by the time the conversion was made to 3.5 they were their own creature. There are certainly similarities, so it is possible that illithid were an inspiration for the VO. The PCs never encountered VO during the 3.0 campaign, so it is a moot point.
The VO are preternaturally psionic, which is explained (up to a certain point) in the PCI book Psionics Unbound, which was written for D&D 3.5. It is (was?) markedly different than regular psionics. The main differences under the 3.5 rules were:
1. Preternatural psionics ignored the first 10 points of Spell Resistance a creature possessed, but Power Resistance worked normally.
2. Preternatural psionics could not be detected by non-psionic forms of magic (for instance arcane or divine spell casters using detect magic). Similarly, preternatural psionics could not be used to detect non-psionic magic.
3. Preternatural psionics continued to function normally in areas of dead magic/antimagic. Areas that specifically suppress psionics also affects Preternatural psionics. Preternatural casters can suppress psionics, but not non-psionic magic.
The Silence is the name for the forces of Entropy. It has been suggested that this was what Larissa saw when she looked into the future, which caused her to go insane and become hedonistic. By and large Henry has maintained a lot of mystery surrounding the Silence. We know that the VO work for the Silence, but if I remember correctly, there is more to the Silence than just the VO.
The VO did pop up during a few combats in the old campaign, and at that point I believe most PCs were around 18th level. Like any species, there are high level and low level versions. One VO is far less dangerous than dozens or hundreds of them. There was a VO at this year's BI, which was imprisoned in the cell block in Tultipet. While I wasn't at that table, my understanding is that it didn't get involved in the combat. When the PCs were rescued all of the cells had to be opened simultaneously, which released the VO. Don't worry, I'm sure that won't come back to bite us in the ass later
It is known that preternatural psionics can be granted to creatures. It was possible through the Mist Wanderer class for Mourners in Silence to gain preternatural psionic abilities. I don't know that it was ever explained what the exact process was, but any race could become preternaturally psionic (not just vals).
At the end of the day, it is possible that some of this is no longer accurate, as there were certain changes in the transition from D&D to the current system. Nonetheless, if you can get your hands on a copy of Psionics Unbound, it is a good read.
Fun fact, the val'Virdan Nierites of Canceri have a tradition of Silence Hunters...in fact, one of the Nierite cities, The Vrain, is an underground complex of caves which were once a VO stronghold.