Adding the script just adds a file to the image.

if you want it to be executed you have to add it to the .script block.

e.g.
[+script] .script = {
# Initialise the console
    procmgr_symlink ../../proc/boot/ldqnx-64.so.2 /usr/lib/ldqnx-64.so.2
    devc-sermx1 -e -F -S -c80000000 0x021E8000,59

    waitfor /dev/ser1 4

    reopen
    display_msg Welcome to QNX Neutrino 7.1 on the Elsinor Hamlet 2B ON2B (ARM Cortex-A9 MP Core)

    /script/my_script.sh & # <<<< execute my script.
    [+session] ksh /proc/boot/.console.sh &
}

[perms=0555] /script/my_script.sh={
#!/bin/sh
echo Hello World.
}