It's not recommended to run the installation process during the day but no, your GP users are accessing different tables than what are created during the QES install so installing during the day is not usually an issue. Because the QES upgrader creates a new database as well as users, tables and other objects on the SQL server it’s highly unlikely (but statistically possible) that something might go wrong during the install.
That being said we suggest running the installation process at night after full backups have been taken. This is so if you had to restore from a backup for any reason, user transactions would not be lost. i.e. accidentally installing QES tables to the wrong company database.