Is the #disabled form element property different from the html disabled attribute? Looking at the documentation for #disabled in the form API documentation, one finds this:


  Setting #disabled to TRUE results in user input being ignored,
  regardless of how the element is themed or whether JavaScript is used
  to change the control's attributes.


If I'm reading this correctly, this seems to indicate that this is different from the HTML disabled property.

If I want to make an element disabled, to later enable it via javascript, and have its value come through in $form_state['values'], I should not use this?
Yes it's different, as well as rendering the attribute the form API also ensures server-side validation is taken care of.

As with all Drupal form manipulation, the right way to remove the disabled attribute is with the Ajax API, not by manipulating the input directly with JavaScript.

Once you use that method, you'll be able to get values for the input(s) in the form state as normal.