Trying to answer this question without straying too far into medical science, philosophy, or dictionary definitions is complicated. I think it might be easier to use terms a little less associated with psychology, specifically psychoanalytic Drive Theory.
For conscious decisions, I'll call this free will. And for "subconscious choice" I'll use underlying cause (or decision). Whether these are fair synonyms is certainly open to debate, but I feel they minimize confounders as above. A term frequently used with homosexuality is latent. I won't use that either.
An example above was breathing. Breathing is involuntary, it happens whether we want it to or not, but we can use our free will to alter the rate, volume, and mouth v. nasal. Involuntary actions and reflexes are related to genetics, and I don't believe them to be synonymous with subconscious.
You asked, Can a choice be subconscious?
Let's use a classic example of the husband having had a bad day at work, comes home, and kicks the dog for a minor slight. His wife asks, Why did you do that?" The guy says, "I wasn't really thinking about it. It just happened. I hope I never do that again."
So even if claims he wasn't using free will in his decision, the underlying cause is obvious. The man is still culpable for his decision (without getting into legal logistics). In order for him to promote a kick-free lifestyle, he needs to do something prior to coming home to arrive with less aggression OR his wife can keep the dog in a separate room.
In this regard, there is still a choice. One would hope the man develops the free will to avoid kicking the dog even under the most stressful of times. However, by being proactive, even an underlying decision can develop the nature of free will by altering the variables responsible for the action.
With regards to homosexuality, there are some clearly making free will choices, such as bisexuals and the transgendered (obviously some will disagree with me but whatever), and there are those who have never found a member of the opposite sex attractive in their life.
In the latter, I find the underlying cause, the "subconscious choice," to be unknown. The free will choice is whether or not to engage in sexual relations.
To answer your question, yes, there are subconscious choices, but they must be separated from reflexes or involuntary actions. If a man has never found a woman attractive, how can his homosexuality be a choice on any level? If a man comes home and kicks his dog, there are things that can be done to promote a different action.