Yes, a penalty shootout counts as a win in betting. If a bet is placed on a team to win and they win the match in a penalty shootout, the bet is considered a win.
Statistical record. A shoot-out is usually considered for statistical purposes to be separate from the match which preceded it. In the case of a two-legged fixture, the two matches are still considered either as two draws or as one win and one loss; in the case of a single match, it is still considered as a draw.