I seem to recall I had problems way back around 5.3 doing this. I disabled CCK I think it was and tables such as content_type_XYZ in my db were eliminated, together with the content in them. Am I remembering correctly?
Can't say if it's correct or not, but I don't actually change themes nor disable mods when I do a 'minor' update of core Drupal. It may be risky, but I have never had a problem. But yes, disabling some modules will IIRC remove tables and therefore data.
Either way, always do the whole process on a spare site, or at the very least, backup your files and DB first. :)
Good luck