Try it or else why don't you take buses from Madgaon or Ponda ?
But please don't test General compartments of this train except in June and July even if you get a seat at Vasco you will have trouble while getting down, even SL is pathetically crowded in this train.
KSRTC buses are much better than this train for Vasco Hubballi route. Plenty of them ply from Vasco and Panjim to Hubballi all go via Ponda and the Vasco ones also touch Madgaon but not the Panjim ones.