There are few reasons why a sap hana administrator will proceed to a standard user deactivation. The common one would be that a person has left the company and will be back months later. There is no reason to keep the user account available all that time. There could be a security issue.
Another reason would be related to a direct security threat from a particular user.
As far as sap recommendations and best practice, the SYSTEM user should be deactivated.
In that case, make sure you have a specific manager user in place before to proceed with SYSTEM deactivation. A user with "USER ADMIN" privilege.
Otherwise, in the worse scenario, you are going ahead to trouble such as hours of service interruption in order to reinitialize SYSTEM USER.
Note: pratical events have shown that, in some cases of database issues, a SYSTEM user being locked has been a source of problem in the first place.