Speaking for me personally (and also as someone who has their own chronic health issues), most of it is, as someone mentioned in the replies, script failure. Humans have a lot of scripts and shorthands for social interactions, and the most common one for finding out someone is ill or injured is to wish them a swift recovery. There isn't really a script for how to respond when someone won't recover tho, and so many people end up falling back on the script they do know even if it's not really applicable.
In my own personal experience, when I end up saying - or feeling the impulse to say - 'get well soon' to someone with a chronic condition, what I'm really trying to convey is something more along the lines of 'I hope your good days outnumber the bad ones', and 'I hope you find treatment that is effective for and accessible to you', and especially 'hey the fact that you are in pain sucks and I wish you weren't but I know that's not likely to change soon but also I hope that it will anyway because I hate to see people suffering and the 5-year-old inside me is insisting it's not fair even though the adult me knows that's not how it works but anyway the point is I hope you're in as little pain as it's possible for you to be in'. All of which is quite a bit harder to fit on a greeting card than 'get well soon', and which don't have any conveinent shorthands that will let me express those sentiments in a concise, understandable manner.
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