Well, I don't think sexual orientations are always so cut and dry as that.
Considering that she was completely female at the time he fell in love with her, and that they were no longer in a relationship after the lifesaving operation that somehow changed her gender (which actually makes
no sense whatsoever, but let's not let that get in the way of a good story
), I'd say that Blackjack is primarily heterosexual.
The fact that they still seem to have some feelings for each other is more under a special circumstance in that a part of Blackjack probably always see's him/her as the woman he once loved rather than the "Man" he/she supposedly became.
But, I'm no expert on Blackjack. So, one of the more hardcore BJ-fans here could probably give you a better answer.