Whether you're in native or mixed mode should have nothing to do with the Netapp's, since the netapps are not domain controllers, and native mode just means that you can't have NT 4.0 domain controllers. Being in native mode does not mean that all your clients must be win2k...

http://www.2000tutor.com/tutorials/modes.htm

From a white paper at http://www.netapp.com/tech_library/3113.html

Filers may be installed into either mixed-mode or native-mode active directory domains. Mixed-mode domains resemble the Windows NT or pre-Windows 2000 domain environments. Native domains use and expose the active directory infrastructure. Both domain styles support pre-Windows 2000 computers. The difference lies in the administrative structure and methods.

The filer will attempt to sense what type of domain exists on the network. Filers running Data ONTAP 6.1 will first search for an active directory domain controller by querying DNS for an active directory/LDAP server.* If the filer cannot locate an active directory server, it will default to looking for a Windows NT domain controller using the NetBIOS protocol. Filers may also be specifically configured as a Windows NT domain or an Active Directory domain file server.