Regardless, the parallels were many. The Hrud were described as scavengers, and carried Jezzail-like rifles called "Fusils". They used warp-plasma-based technology, and apparently lived in underground tunnel systems. At the time, I think it was very clear these were originally intended to be Space Skaven.
Apparently even way back in the Rogue Trader era, Skaven were being seriously considered as an addition to the setting. In 2001 Black Library published The Gothic and the Eldritch: The Collected Sketches of Jes Goodwin, which included concept art for 40k Skaven (scans courtesy of Jon Boyce):
Xenology pictured a new type of Hrud, scientific name Troglydium hrudii:
Some very interesting ideas that don't seem quite fleshed out yet, but this effectively ended any chance of the Skaven showing up in the 40k setting for the time being.
But "when one door closes", as they say...
And back in our world, NASA is making its own plans to get rodents up into the stars...