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The topology of the SAN (FC or Ethernet iSCSI) is irrelevant to your question. It will work the same with either. ArcServer 2000 and Windows 2003 (I assume you mean 2003 and not NT since Microsoft no longer supports NT) work similarly when connected to the SAN. Each sees its tape library or disk storage as if that storage is directly connected to the server. The issue here is that the SAN storage device can be shared.
Both ArcServer 2000 and Windows 2003 have the ability to work seamlessly on the SAN. The advantage of the ArcServer is that it can backup data from other servers (other than just Windows) over the TCP/IP LAN, then to the tape or disk on the SAN.
The SAN is not your issue. The backup software choice is your issue. It should be decided based on its ability to meet your organization's disaster recovery and business continuity needs and your budget.
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