Watching the episode again, it turns out the edge of the shockwave hits Voyager after about 20 or so seconds. (I didn't time it). Janeway orders Paris to stay ahead of the "brunt" of the wave. So it would appear that the edge of a supernova's shockwave is FTL. Whether the "brunt" is also FTL (but slower) or STL is unknown.
KIM: That's the edge of the shock wave. The pressure's over ninety kilopascals, thirty percent more than we predicted.
JANEWAY: Tom, back us off at full impulse. I want to stay ahead of the brunt of that wave.
Also it is unknown whether TOS' "All Our Yesterdays" has this same problem. TNG's "Generations" also had a nova event but the shockwave was definitely sublight (although it's been a while, did the leading edge of the shockwave reach E-D at FTL speed?)