You'd think this would be easily verifiable, considering his ship has some powerful computer inside. Plus I believe it was said he had to travel for millennia, so millions of years are right out. And millennia wouldn't be enough to completely erase all traces of our existence - obvious archaeology aside, our stone monuments would take hundreds of thousands of years to fully erode. So unless the mangaka didn't even consider such things I'd say it's unlikely.
Not sure if a millennia was ever mentioned in the manga, I don't recall that being mentioned, but going through the story again, Chapter 3:
"I'm no astrophysicist, but if Hitoshi's words are to be believed, his planet is likely already gone, as his journey itself seems to have exceeded its lifespan."
If Hitoshi was frozen, suspended animation, cryogenic state, whatever you want to call it, for 1000 years (the time you say he travelled for), and his ship was travelling at 99.999999% the speed of light, approximately 2.24 million years would have passed on Earth.
Earth will become uninhabitable in about 1 billion years when the temperature from the Sun rises enough to burn off all the water from our planet, and totally destroyed when the Sun becomes a Red Giant and its size grows beyond our current orbit in about 4 to 5 billion years.
That's plenty of time for a couple million or so years to have gone by, current animal life to evolve, and humans and thier society as a whole to have long died out without much of any remnants left, as well as the continents to have shifted to look different enough,
and the planet still being in the habitable range. 2.24 millions years is a drop in the bucket compared to 1 billion years.