What's the difference between adding scripts in the /etc/cron.daily/ or editing in your script in crontab(-e)?

The system-wide scripts in /etc/cron* are world-readable by default. For example, on my Arch:

$ ls -ld /etc/cron*
drwxr-xr-x 2 root root 4096 May 31  2015 /etc/cron.d
drwxr-xr-x 2 root root 4096 May 31  2015 /etc/cron.daily
-rw-r--r-- 1 root root   74 May 31  2015 /etc/cron.deny
drwxr-xr-x 2 root root 4096 May 31  2015 /etc/cron.hourly
drwxr-xr-x 2 root root 4096 May 31  2015 /etc/cron.monthly
drwxr-xr-x 2 root root 4096 May 31  2015 /etc/cron.weekly

And:

$ ls -l /etc/cron.d/0hourly 
-rw-r--r-- 1 root root 128 May 31  2015 /etc/cron.d/0hourly

User-specific cron files are in /var/spool/cron by default and they, at least on my system, are not world-readable:

$ ls -l /var/spool/cron/
total 8
-rw------- 1 root   root   20 Feb 23 16:34 root
-rw------- 1 terdon terdon 22 Feb 23 16:32 terdon

So, the "safest" way would be to use the user's crontab, the one you get with crontab -e. Normal users can't read that:

$ cat /var/spool/cron/root 
cat: /var/spool/cron/root: Permission denied

I suggest you check and make sure this is also the case on your CentOS first though, I don't have access to a CentOS machine at the moment.