Certainly some sentient phenomena in the Trek universe seem to be treated in inhuman ways. But for example the Moriarty case raises the issue of value judgement: for some of these alien intellects, being treated humanely might be a fate worse than slavery or death.
Moriarty was a born and bred villain; would he have found satisfaction if denied the treatment that villains deserve? At the very least, treating him humanely would be like forcibly raising a promising child to be a chess master or a marathon runner against his or her wishes and dreams. At worst, it would be akin to making a slave pull a plow because his limbs and back make him suited for it, even when they have other, more natural uses.
Starship computers might well be sapient, sentient and rather prissy - but they seem perfectly satisfied with their lot. Even at worst, their life seems analogous to that of a house servant, but probably is no different from the jobs of Kirk or Worf or O'Brien. If kicked out of their jobs and set free, they might feel like a patient doomed to a life in an iron lung.
Really, the Judeo-Christian mythos and work ethic on which Trek, too, is based would have us believe that life is hell and a better fate awaits after death. But some of these artificial intellects may already be in their form of heaven. If these lifeforms are superior to humans in basically every way measurable (lifespan, intellect, memory, imagination, perception of environment etc), giving them human rights would mean hacking off their limbs, gouging out their eyes, nailing the torso to a dirty board and saying "now you must be really happy because you enjoy the same freedoms we do".
Did the EMH Mk Is feel unhappy doing forced labor? Probably, since they were specifically programmed to mimic human reactions. But they could enjoy lives superior to human ones while mining - they could write and perform a thousand operas with each swing of the phase-pick, or have wonderful sex between themselves with each dilithium shard knocked off the bedrock. And they could be programmed (or self-programmed) to really, really enjoy mining.
And that's with the most humanlike of these alien intellects. To impose human values on the rest of that bunch goes way beyond telling a Vulcan to lighten up and knock down a few beers on the pain of death.
Timo Saloniemi