Disabling modules anyhow can certainly lose data. Even without uninstalling. I disabled the Ads module on a site once, I believe, and data was lost which we were forced to restore (what we could) from backups.
If it does the module is broken and needs a bug report issued. I've not found this case.
I believe I made a mistake. The case where I lost data I think was actually that I uninstalled a module.
You are correct, because simply disabling module does run any code, so how could any data be lost?
It indeed should be the case that disabling modules will NOT lose any data.
My mistake for saying otherwise.
Fred