You can update it like other plugins whether you manually disable it or not. However if you disable it you will miss your current configurations.
HMWP updates htaccess file but these changes doesn’t make any problem for your site. (Even if HMWP was disabled)
You can use any standard text editor to edit htaccess but if you did it, please note you should choose ‘customized htaccess’ option in HMWP settings page. This tells HMWP that should not update htaccess automatically.
PS:
Be careful about it, any syntax error in htaccess will break your entire site.