Option “-e” is deprecated and might be removed in a later version of gnome-terminal in Ubuntu 18.04

Read the error message:

# Option “-e” is deprecated and might be removed in a later version of gnome-terminal.
# Use “-- ” to terminate the options and put the command line to execute after it.

The error message tells you that -e is deprecated, and may be removed in future versions, and the alternative to -e.

You have the following command line:

Exec=gnome-terminal -t "Disk Manager" --hide-menubar -e "df -h -- output=source,used,size,avail,target -x devtmpfs -x tmpfs -x squashfs"

Change this to

Exec=gnome-terminal -t "Disk Manager" --hide-menubar -- "df -h --output=source,used,size,avail,target -x devtmpfs -x tmpfs -x squashfs"

You want:

gnome-terminal -t "Disk Manager" --hide-menubar -- df -h --output=source,used,size,avail,target -x devtmpfs -x tmpfs -x squashfs

-- is generally the universal command line syntax for "nothing after this should be interpreted as an option". In this case, GNOME Terminal just takes any arguments it's given and executes them as a command line, with the first argument as the program as the rest as the program's arguments.

-- "df..." failed because it was using the entire command line as the executable name.

I've could use -- with command that contains parameters (remember remove doble quotation marks which surround the command to be passed to the terminal. Otherwise it will fail)

Exec=/usr/bin/gnome-terminal -- globalprotect connect -u $USER_VPN -p $VPN_TO_CONNECT

This worked fine for me. Execute the complete line in your terminal (avoid the Exec= part obviously) before save the file to check if it's working as you expected or not and so save time.