LaunchAgents run as the user. LaunchDaemons run as root. As you are running the command via Casper, the script runs as 'root' and unloads notification center for the root user. When you run the command yourself, you're running it as the local user and not as root.

Try this DerFlounder post about running the script as the user.
https://derflounder.wordpress.com/2016/03/25/running-processes-in-os-x-as-the-logged-in-user-from-outside-the-users-account/

Thanks so far i created this script:

!/bin/bash

Identify the username of the logged-in user

logged_in_user=python -c 'from SystemConfiguration import SCDynamicStoreCopyConsoleUser; import sys; username = (SCDynamicStoreCopyConsoleUser(None, None, None) or [None])[0]; username = [username,""][username in [u"loginwindow", None, u""]]; sys.stdout.write(username + " ");'

Identify the UID of the logged-in user

logged_in_user_uid=id -u "$logged_in_user"

/bin/launchctl asuser "$logged_in_user_uid" unload -w /System/Library/LaunchAgents/com.apple.notificationcenterui.plist

exit 0 ## Success
exit 1 ## Failure

When running this script i see the following message: User$ /Library/Application Support/JAMF/Composer/Sources/Disable.NotCentre.2016/Scripts/postinstall ; exit;
This subcommand requires root privileges: asuser
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.

[Proces voltooid]

What is the right command to use to accomplish this or is it just not possible on el capitan?

I found the right script here: https://jamfnation.jamfsoftware.com/discussion.html?id=9902

Credits to Josh.Smith

Script:

!/bin/sh

postinstall

Get the logged in user's username

loggedInUser=$( ls -l /dev/console | awk '{print $3}' )

Get the logged in user's UID

loggedInUID=$(id -u $loggedInUser)

Use the above to

/bin/launchctl asuser $loggedInUID sudo -iu "${loggedInUser}" "launchctl unload -w /System/Library/LaunchAgents/com.apple.notificationcenterui.plist"

exit 0 ## Success
exit 1 ## Failure

Does anyone know if it's possible to run the above without logged in user account?

Maybe my knowledge of scripting isn't very good but i managed to disable notificationcenter without user interaction, once disabled all required stuff will be removed on next reboot.
If someone with more scripting knowledge knows a better/simpler way to accomplish this then please share your thoughts.
I created the following and used composer to create the package:

/Library/LaunchAgents/local.disablenotcenter.plist

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict> <key>Label</key> <string>local.disablenotcenter.plist</string> <key>LimitLoadToSessionType</key> <string>Aqua</string> <key>ProgramArguments</key> <array> <string>/Library/Scripts/DisableNotCenter.sh</string> </array> <key>RunAtLoad</key> <true/>
</dict>
</plist>

/Library/LaunchDaemons/local.disablenotcenter.plist

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict> <key>Label</key> <string>local.disablenotcenter</string> <key>Program</key> <string>/Library/Scripts/DeleteScriptAgentDaemon.sh</string> <key>RunAtLoad</key> <true/>
</dict>
</plist>

/Library/Scripts/DeleteScriptAgentDaemon.sh

.#!/bin/bash
.#Disable Notification Center

doc=/temp/notcenterdisabled.txt

if [ ! -f $doc ]
then

exit 0

else
.# Unload LaunchAgent
/bin/launchctl unload /Library/LaunchAgents/local.disablenotcenter.plist

.# Remove LaunchAgent
/usr/bin/srm -f /Library/LaunchAgents/local.disablenotcenter.plist

.# Remove DisableNotCenter.sh
/usr/bin/srm -f /Library/Scripts/DisableNotCenter.sh

.# Remove Helper Daemon
/usr/bin/srm -f /Library/LaunchDaemons/local.disablenotcenter.plist

.# Remove temp dir
/usr/bin/srm -Rf /temp

.# Make script self-destruct
/usr/bin/srm $0

fi

exit 0

/Library/Scripts/DisableNotCenter.sh

.#!/bin/bash
.#Disable Notification Center

.# Sleeping for 5 seconds

sleep 5

.# Unload Notification Center

/bin/launchctl unload -w /System/Library/LaunchAgents/com.apple.notificationcenterui.plist

/usr/bin/touch /temp/notcenterdisabled.txt

exit 0

Also created a directory in the root and named it temp with read write acces for everyone

Does anyone know a method that does not require turning off SIP?