For me, I can explain what is loud and quiet commentary in fantasy: For instance, the violent white supremacy of the Conan the Barbarian novels is very blatant, I can see that (Robert Ervin Howard was famously white supremacist, even by the contemporary southern standards), on the other hand, the racist ideas of Tolkien's are much more subtle and harder to confront (creating the orcs after the mongols, evoking that old European fear of a mongol invasion).
I know nothing about the Conan novels but I'm pretty sure Tolkien's Orcs were originally Elves, captured and corrupted over time (so not sure how they are supposed to mirror the Mongols if they are simply corrupted versions of the 'pure' ones). Do you have a source that they were based on Mongols? I have never read that before.
I read an article recently stating that Frodo and Sam were in a closet homosexual relationship in the novels. Our contemporary cultural goggles, I think, often skew our vision as to what was intended...and obviously in many cases, shine a new light on them.
Lorewise, you are perfectly right. Orcs were created after Melkor captured, tortured and corrupted some of the earliest elves.
But, I am talking about meta-literary stuff. This is a very common criticism (found in most scholarly analysis of his) that is leveled against Tolkien's body of work, that his concept and depiction of the orcs were heavily influenced by the medieval descriptions of the mongols by European chronicles. So Tolkien, as an English man, wrote orcs as these parodies of Asian people who are invading the white space (Middle Earth).
Of course, I am not saying that Tolkien was an evil man and his work is awful for this. He had issues, sure. But, on a more positive note, he was also a passionate environmentalist and his work is also permeated with that.
On the note of Sam and Frodo, imo they are more of a reflection of Tolkien's experience in the Great War with his comrades in battle. Sam and Frodo mirror a very old literary tradition called the Love of the Heroes (like Gilgames and Enkidnu, Achilleus and Patroclus, David and Jonathan, et cetera), battle buddies with an overwhelming level of devotion to each other. Reading this as erotic is not a contemporary thing however, the entire Antiquity read the Illiad as a love stoy.
So yeah, it is not a stretch to read Sam and Frodo as more than friends. I mean, after Sam's children grew up, he did leave them and Middle Earth behind to find and reunite with Frodo.
"Don’t urge me to leave you or to turn back from you. Where you go I will go, and where you stay I will stay." (Book of Ruth)
Imo, that is love, whether erotic or not that can be debated, but it is a powerful love.