Does having a character turn out to be gay in a sequel make my series unmarketable?

There are YA books with secondary characters who are gay. The Mortal Instruments come to mind.

Pretty Little Liars is another example of a wildly successful YA series featuring a major character who is LGBTQ. The Gossip Girl books also dealt with characters exploring their sexuality in later novels without sacrificing marketability or readership...I think it all depends on how it's handled and what audience you're targeting.

Maybe I'm a little different, but I think I have a lot of characters who are presented as neither straight nor gay, because the issue of who they are sexually attracted to doesn't come up in the story in any way. I write a fair bit of action, so when you're running for your life, strange creatures are invading your planet, or you're fighting off zombies to survive, you might not spend too much time worrying about the sexual orientation of everyone around you.

I think it's the story that should dictate where you go and how you handle it. If the question comes up in the first book, giving some hints is fine, but I don't feel you need to put hints in there just because the issue will come up in book 2. Storylines are great to foreshadow, as are character arcs, but it shouldn't be necessary to foreshadow sexual orientation just because some people assume straight as the default.

I really hope that in this day and age having a gay character isn't an issue on sale-ability. I don't think it is, but it's always been hard for me to wrap my head around the tastes and preferences of pop culture.

Given the number of people who deliberately read banned books, no, a controversial issue like a gay character won't destroy your marketability. The question that only you can decide is, are you willing to embrace the controversy?

I'm sorry, but I think you ought to sell the first book before worrying about the second. If an it's an issue you'll have a team, ie your agent and editor, to help you figure it out.