By default, elementals do not appear to be sapient creatures.
I think before considering the lore of the Eberron setting, we should look at the lore of D&D as a whole. What the Monster Manual says is considered to be true in all settings unless the setting itself specifically contradicts it. While an elemental is slightly smarter than most animals, the Monster Manual describes them this way (MM p.123):
On its home plane, an elemental is a bodiless life force. Its dim consciousness manifests as a physical shape only when focused by the power of magic. A wild spirit of elemental force has no desire except to course through the element of its native plane. Like beasts of the Material Plane, these elemental spirits have no society or culture, and little sense of being.
In addition, the section on creature types (MM p.6) says
Elementals... Some creatures of this type are little more than animate masses of their respective elements, including the creatures simply called elementals.
The Monster Manual seems to be going out of its way to say that elementals aren't sapient creatures, but just slightly willful blobs of elemental energy. Binding one into an elemental vessel is, arguably, merely returning it to the form it takes in its home plane. In any case, the monster manual says they don't really have a sense of self, which sounds like a functionally animal mind to me. (This is all referring only to the abstract elemental creatures that are actually called "Fire Elemental" or whatever; I'm not addressing creatures of the elemental type that are definitely sapient creatures, such as xorns, mephits, or efreet.)
I think the comparison to a trained animal is pretty apt. It's probably important to note that while most beasts have an intelligence score of 2 or 3, there's no rule anywhere that specifies a maximum "animal intelligence" (as there was in 3rd edition). Many creatures that we would think of as simple monsters have INT scores as high as an Elemental's, including Displacer Beasts and Wyverns.
Eberron doesn't say much on the matter.
All that said, there doesn't seem to be a particular statement in any of the Eberron books that directly addresses this point. Clearly elemental binding is considered ordinary and unproblematic to most of Khorvaire, but there are plenty of real-world examples of what we would consider unethical behavior being considered ordinary and unremarkable in another culture.
There are some Ashbound druids who attempt to free bound elementals, but the Ashbound are explicitly fanatics who "consider arcane and divine magic to be unnatural" and "strike at farms and ranches that attempt to confine or cultivate nature" (D&D 3.5e Eberron Campaign Setting, p.75), so they seem less specifically concerned about the rights of elementals than about the use of any form of technology or arcane power.
The people of Khorvaire as a whole don't seem to be concerned about elemental binding, so as far as the setting goes, it seems to be a non-issue.
