Actually, the physics papers I took taught us that you would have to worry about relativistic effects above 10% of lightspeed. Still, if your calculating travel times from acceleration you would probably want to get a computer to calculate it (to allow quick calculations when you change something), meaning that special relativity is easy to account for.
Another interesting result is that under special relativity, any FTL travel is equivalent to time travel . But that is probably hidden in 40k by the ways that the warp screws with time.