Yes, still running/supporting a major system using SQL 2000.

The system uses multiple servers across the world, synchronized with Merge Replication, all containing sensitive data.

The cost of upgrading the SQL licences is (fairly) insignificant. The main thing holding back an upgrade is the sheer cost of planning and testing... not just the upgrade of SQL itself, but a full regression test of the application as well. For that reason, it's worth forking out for paid MS support.

Luckily, as said, SQL 2000 seems to be fairly bulletproof.