Never too late to send a card. Just ignore that you never sent one and send one saying you think about them a lot and how hard the loss must be for them.
I can feel your pain regarding your son's sexuality. Even in this more enlightened world it will not be an easy road to hoe. Maybe you can try to help him to see that it would be better if he not act on his feelings until he is more sure of himself. I think at this time in a boy's life it is not uncommon to feel this way, and sometimes it passes (and sometimes not) but either way, it is probably best not to experiment (I am thinking STDs here as well as what he would do to himself mentally later on, if it turns out to just be a phase) if at all possible.
I am sure that the whole thing with the AP is nothing and mentally you are exaggerating it because you are worried (that is most definitely what I do).
Here for ya, hugs