I investigated this in a new game. I created a human empire, jumped into an adjacent system, then SMed in a new player controlled empire in the new system. The humans saw the new empire and jumped back to Sol. I then SMed in another player race and had them conquer the first race, unseen by the humans.
After the conquest, the humans still had an entry on the intelligence screen for the conquered empire. I jumped their ship back in, they encountered the new conqueror empire, and despite the absence of the old conquered empire, the human intelligence screen still listed them as well.
From this I conclude that the continued presence of an empire on the intelligence screen is not sufficient proof that the empire still exists with active populations. Of course, I didn't do this with computer controlled NPRs, so maybe NPRs do autoprune from the intelligence screen.
