There is an option in settings > general that controls how files are handle if you want to delete files from the server be sure that the option is checked.

1) You create a new gallery, add/change the folder path under the import box and use the scan the folder option or you can just delete the folder.

2) There was a bug in earlier versions where all data in the database were deleted properly, but not the files were not. Deleting the files should be fine.

3) It will be better to leave the alone, but if you want you to check the “post” table and looks for the “ims_gallery” content type.