confirmed

alias php-opcache='/usr/bin/php -d "zend_extension=opcache.so" -d "opcache.enable_cli=1"'

php test.php
int(3)

php-opcache test.php
Notice: Undefined index: nsno in test.php on line 7
NULL

FWIW: Happens only with the '$GLOBALS = array();'

there must be something corrupt because you can't even detect that in code - !isset($GLOBALS['bug_78961']['nsno']) don't fire the line before - was attempted to write some regression test for it

<?php declare(strict_types=1);
switch (1){
    case 1:
        $GLOBALS = [];
        $GLOBALS['bug_78961'] = [];
        $GLOBALS['bug_78961']['nsno'] = 3;
        if(!isset($GLOBALS['bug_78961']['nsno']))
        {
         trigger_error('https://bugs.php.net/bug.php?id=78961');
        }
        var_dump($GLOBALS['bug_78961']['nsno']);
    break;
}

Due to commit 3ccd3ab[1], CSE optimizes this basically to

    $GLOBALS = array();
    $GLOBALS['td'] = array();
    $td['nsno'] = 3;
    var_dump($GLOBALS['td']['nsno']);

However, $the assignment to $GLOBALS severed the link to the
global variables, so that this optimization can not work.

The switch is irrelevant, by the way.

[1] <http://git.php.net/?p=php-src.git;a=commit;h=3ccd3aba90b4c0c95f1e0a457dbbc33c4524a4ed>