I imagine Bubbles probably meant it in a platonic sense - but only realized how it sounded after she said it...
I would imagine that if that were the case, the two of them would find it easy to laugh off. Not without making Bubbles a little embarrassed, but still. It could be that this is exactly what will happen in the next comic. That said, the fact that they both reacted in that same way to me seems to indicate that it's something they both already had been thinking about. Or maybe trying not to think about.
It really doesn't seem to be likely, as much as Jeph is teasing us about it. Faye's entire history is opposite-sex relationships with carbon-based people despite having a synthetic interested and available for years. Bubbles hasn't shown any sexuality that I can remember. I'm open to getting surprised. It would be the most interesting relationship to explore in the history of the comic.
Who is the willing synthetic in question? I suspect you mean Pintsize, but I don't think he has any serious interest in Faye. I think his sexuality is a lot more complex than could be satisfied with any traditional relationship anyway. He seems to get off on things that humans don't even recognise as... things. Which is very much to be expected from at least some AI, in my view.
As for Bubbles, you're right that she's not displayed much signs of sexual interest, but it could be that she's just very, very private about such things and wouldn't let anyone know. It could also be that she's not used to that kind of feelings and doesn't know how to process them.