Hi
There are two kinds of non interactive users: Communication & System (see note 622464 - Change: Password change req. entry for "SYSTEM" user type).
System type users cannot change password thus it should not be affected.
Also make sure to set parameter login/password_compliance_to_current_policy to 1 (862989 - New password rules as of SAP NetWeaver 2004s (NW ABAP 7.0))
I've done a quick test and in fact system type users with non compliant password are not affected by password rules changes, even if login/password_compliance_to_current_policy is set to 1.
Regards