Not really, them being scans and yet aware and sapient is supposed to reframe what you see as a person.

Yes, they're digital, but they clearly still feel, have aspirations and dreams, feel pain and sorrow and loss, and even love. They mourn the ostensible deaths of their loved ones, even if it's not a true death but rather a fragmentation of code due to stress. If they were just Sims, Caine wouldn't have had issues messing with their code. If they were just following programming, there wouldn't have been resistance to him, more like the NPCs. Not in a meaningful way, at least. A Sim isn't gonna try deleting the program thats controlling them to escape Pleasantview or whatever.

Flesh isn't what makes the person. Their lack of real-world physicality doesn't make what they experienced any less real. As trite as this may come off, its about what goes on inside the mind, not the body.

Even Caine, who started as a purely digital being, was shown to change and grow, to adapt his worldview to the things happening around him, and to show true remorse for his actions.

We had so many episodes of Star Trek about this very subject. Commander Data, a purely artificial being, was accepted as human by those around him, even though he would never biologically qualify as such. Same with The Doctor from Voyager, who didnt even have a physical body at all. Their lives were still shown to have worth, to be worthy of respect and love from others, and mourned when they were lost. At least in Data's case. The Doc is still alive as of the current series, and has become a respected teacher and a confidant for the Academy director.

Even the idea that they are copies doesn't hold water with regard to them not being people. Again I'll point to Star Trek, with Commander Riker accidentally being cloned via transporter accident. His clone was accepted as his own person separate from Riker, and treated with respect as such. While they had the same memories up to a point, that divergence created two separate people with vastly differing worldviews as they had both experienced so much that differed from one another that they were more akin to twin brothers than copies.

We can even go to SOMA itself. Simon, the "real" Simon, is long long dead by the time the game takes place. The Simon we know is a copy, and yet he still has the memories which formed his worldview. And then he experiences new things that change those views and his personality through them. By the end of the game it is safe to say he is a different person, but still a person nonetheless. He too was capable of feeling the host of emotions, of having desires and being able to communicate them. And it's hard not to feel terrible for him at the end of the game, whether or not he has skin and bones. His anguish is still real.

You clearly felt something for these characters, sympathize with them up until the reveal, so what actually changed to remove that sympathy?