What happens when a module is installed is the language file gets read. Any strings that are found are moved into the database so they can be over-ridden from the ACP.
If there is already a language string for the corresponding number in the database, its not updated.
So if initially you have
$lang[55] = 'System Updates';
and you change that in the language file, it will see that string 55 already has an entry in the database and not import it.
this is the reason I chose to start from $lang[1000] for your suggested additions. That will leave all the spaces up until 1000 free for the module to use.
Even if you do update the module, the language strings are now in the database so they will survive updates.
The only time I can think of where issues will arise is if that module ever gets to 1000 language strings and tries to enter 1001 but you have already claimed that position with your strings, so the modules ones wont get into your system.