Thargoids notwithstanding, every character we've seen in the Elite games is (or can be assumed to be) human, broadly speaking.
But some of the fiction - and I admit I've not read the ED tie-ins yet, but am relying on my memories of the Frontier fiction anthology - indicates that the universe is full of life. I honestly can't remember if any of it was intelligent, or just xeno-fauna.
So - are there any nonhumans in the expanded universe?
(My reason for asking is that I'm working on an OC for fiction who's basically an uplifted orang-utan. Planet of the Apes and Terry Pratchett references may lie ahead.)
Short answer - no with a but, long answer - yes with a but.
In Original Elite, as you say, glaxy was teeming with life and sentient life (it was basically Star Trek and humans were just one type).
In ED all the past games have been heavily retconned, we have the obvious ones: Thargoids - alive, and Guardians, dead for 1-2million years, probably.
However, in ED Lore (but not actually 'seeable' in game other than descriptions) there is a few other sentient species explicitly mentioned:
"The system of Achenar was chosen for the outdoor world orbiting one of its gas giants, already capable of supporting human life, now known as Capitol. There was already life on the planet and though Duval didn’t know it at the time, one of the few known sentient species watched their landings.
Back then, life was known to be plentiful throughout the galaxy, though it wasn’t appreciated how rare sentient life was. Before long the species was made extinct by the settlers, mainly through imported bacteria. Much later, this extinction would later be used as a pretext for Federal intervention in the system."
Source: Galnet
https://community.elitedangerous.com/en/galnet/12-JUL-3301
Ophiuch Exino Artefacts (rare Commodities)
"These strange sculptures are believed by some to have been created by a now extinct ancient sentient race. Others have theorised that the sculptures are a natural formation caused by local weather patterns. Most economists agree that there are massive profits made from the gullible and wealthy collectors."
Soontil Relics (Soontil Aliens)
These alien artefacts were confirmed by Chief Xeno-Chemist Lyran Betar to not have been made by human hands and date back tens of thousands of years.
Galnet
https://community.elitedangerous.com/en/galnet/18-MAY-3301
There are numerous references to AI - which may have been sentient and gone rogue, although there's no specific proof.
There are also numerous references to plant-life, animals and things on other planets, so yes, tons of alien life, not much (known) sentients:
David Braben said "If you look at galactic history and life on Earth, as a percentage of time it has taken hundreds of millions of years to evolve and a small number of millions of years to evolve sentient intelligent life. By the 21st century humans are not a space faring race yet. So even by the 34th century it's still a tiny slice of time. You can imagine different populations spotting up and you wonder how long we will last which is slightly depressing, but you know we might go beyond. The point I'm trying to make is the chance of two races that are at the point of being able to interact whilst both are still alive is actually small. This is the basis for the story, because the beauty and interesting thing with things like artifacts and unknown probes is that it creates wonderful speculation and that great feeling of discovery. There's a lot of interesting things in the history of the game such as the Thargoids which are mysterious and very dangerous, that have been in previous games, even interacting with them and then suddenly disappeared. So there are a lot of interesting mysteries such as the alien ships with hyperdiction. In the previous games the Thargoids have been a very powerful race. We don't know whether the sightings are real or manufactured. We don't know how peaceful they are so we have to see how that pans out. This is perhaps the first story where millions people interact with the same story. Where people on all the different platforms are cooperating or competing with each other in the same servers and story. How the story unfolds is determined by how players react and what they do."
https://www.youtube.com/watch?v=XTtiGxJIFyM
Michael Brookes said in the Elite: Dangerous Fiction Diary #1: "Alien life in the galaxy is very plentiful. However, sentient life is very rare. So the various races and types of indigenous that was reported in the original elite are considered a dominant species of their planets, but they aren’t sentient species. As far as humans are concerned they’ve only encountered a small number of sentient species. There was a sentient race on Achenar which the people who later became the Imperials wiped out. There’s the alien artifact that was discovered in the solar system. That’s a mystery although we hope to reveal a little bit more about where that came from in the future. And, of course there’s the Thargoids"
https://www.youtube.com/watch?v=O6z5OK8J5pg&feature=youtu.be&t=9m34s
