I had to look up what year he joined Scientology. It was in 1990 thanks to his then wife Mimi Rogers.
Before Scientology, onscreen he behaved and had the vibes of a more or less typical young guy but, after joining Scientology, the further he got into it, the more robotic and fake he became both onscreen and off.
His appearances on Graham Norton (one of which I was watching again recently) are very EXTRA! Every word and every movement seemed very scripted and very self-conscious. It's the behavior of someone who knows they're being watched.
Even on "fun" talk show appearances, he never lets you in with a glimpse into his true self like other actors do.
Just compare him to another Graham Norton guest Helena Bonham Carter. She's nuts too but she's endearing and seems at ease even though she probably loathes doing publicity. She's being herself. Not putting on a self-conscious performance.
Below is a photo from 1983 of him and his Risky Business co-star Rebecca De Mornay.
They were dating at the time but I've noticed, even though he looks more natural in those days and they had amazing chemistry in the movie, the body language between them while out and about in public as a couple for two years after the movie seems more like they're just friends or even siblings.
The only photos of them (that weren't from the movie or were publicity shots for it), the only touching they do is holding hands. More often than not he's completely removed from her and either has his hands behind his back or clasped together in front of his crotch.
There are photos of him walking way ahead of her in the street. I couldn't find any photos of them with his arm draped around her shoulders or the pair of them with their faces lose together like you see with regular couples (especially young horny ones).
I also found photos of him and another "girlfriend" Heather Locklear.
I could only find photos from three separate events (based on their clothes). At a glance, they seem like a cute couple but then you notice the body language and they look more like polite work colleagues at an office function.
Compare their body language to when Heather was dating Tommy Lee or Richie Sambora. She was all over them and you can tell their love was real.
Same with Rebecca De Mornay and her later lovers - plenty of photos of her head resting on her man's chest, arms wrapped protectively around each other, adoring looks exchanged.
Neither had that with Tom.
So I'm going to say he's asexual. He may or may not be gay but he definitely has intimacy issues both physically and emotionally.
Don't forget, Tom went to a seminary for a year but got kicked out for reasons unknown.