it doesn't affect stamina and FT training. Stamina and FT are team training and players automatic gets +48min for training. That means that players doesn't need to get +48min in game and he will get full training.
well, from game manual for standings:
Ties in the standings are broken first by number of forfeits (indicated by a * next to the number of losses a team has), followed by point differential, then points scored.
so, if team has forfeits it would be ranked lover than team without forfeits and should have bigger draft pick. I don't think that there are penalties in draft pick if someone forfeits games.