Nothing makes you feel more secure when hurtling through the void of space like a spaceship decorated with skulls. The skulls go well with the red velvet floor covering. Wait a minute, that's not velvet!
But in the early editions of 40k 1000 psykers are sacrificed every day to keep the Emperor powered, the Emperor trapped at the threshold of life and death, doomed to endlessly battle all the chaos gods and hold back the warp by keeping a good portion of their attention and power elsewhere. And by the time of 40k. He's been at it 10000 years.
So yeah. They got skulls and bones to spare... (And maybee they act as a sort of psychic insulation against the warp? Thats a-lot of Psyker knoggins!)