It is not common practice to disable the ignore_user_abort function, nor does it have any security implications.
The ignore_user_abort function is meant for command line PHP cases. Normally, when a script is run and then the terminal disconnects while it is running, the script will continue until it tries to produce output, at which point it would be terminated. Using the ignore_user_abort function allows that to be disabled, so that the script can continue running in the background.
The only potential security implication is having a script able to be run leading to a denial-of-service attack, however, this is not a real security issue. A script that produces no output will run regardless, so disabling ignore_user_abort doesn’t affect any meaningful real-world cases.
There is no valid reason for a host to disable the ignore_user_abort function.
That said, the use of it in wp-cron.php is only meant for cases where the wp-cron system is rigged up to a command line. This is not the default or normal case, and if you’re seeing the message from it being run by http, then the ignore_user_abort function does absolutely nothing. So it makes no difference whether the line is there or not. You can re-enable ignore_user_abort, or just remove that line from wp-cron.php. It’s not a good idea to edit core files, but in this case, that line makes zero difference to the functionality of the file.