Somewhere along the way the message has been lost, and from where I sit it's due to a lack of communication between clinicians, bean counters and IT people. Clinicians often have a rather arrogant view of the world. They tend to assume technology is easy and the only reason they can't do it is that they haven't been bothered yet. The don't treat IT professionals as being specialists in their own right. Rather, they treat them as service people, in much the same way as you would pay someone to mow your lawns (it's menial and I don't have the time blah blah...).
On the other hand IT professionals (the ones that do the UI stuff) rarely seem to understand or care why the data is being collected, just that it is. This of course leads them to make all sorts of assumptions that often turn out to be completely incorrect. One such system that I've seen had 2 options for gender, male and female. This system was supposed to be used in a urology department that often dealt with intersex people.
Finally we come to the bean counters, for some reason healthcare and healthcare IT seem to attract the worst of the worst PHBs which just compounds the entire problem.