How does Drush figure out modules that have updates?
Use pm-uninstall to completely remove a module from your system.

If you have already deleted the code for the modules in question, the safest and best thing to do is put the code back and run pm-uninstall.  If you just want to get rid of the reference to the module in the system table, you could take matters into your own hands, and just do this:

drush sqlq "delete from system where name in ('moduleone', 'moduletwo');"

If you do that, though, then the module won't have a chance to remove any other unneeded assets that would be deleted if you used pm-uninstall.