Edit the command to:
updatedb --require-visibility 0 -o ~/.locate.db
from "updatedb (8)":
-l, --require-visibility FLAG
Set the 'require file visibility before reporting it' flag in the generated database to FLAG.
If FLAG is 0 or no, or if the database file is readable by "others" or it is not owned by slocate, locate(1) outputs the database entries even if the user running locate(1) could not have read the directory necessary to find out the file described by the database entry.
If FLAG is 1 or yes (the default), locate(1) checks the permissions of parent directories of each entry before reporting it to the invoking user. To make the file existence truly hidden from other users, the database group is set to slocate and the database permissions prohibit reading the database by users using other means than locate(1), which is set-gid slocate.
Note that the visibility flag is checked only if the database is owned by slocate and it is not readable by "others".