Are there any tools especially designed for very large/complex domain/database models? I am speaking of 200+ or 500+ entities/tables?
Common standard tools don't cope well with this amount, both in terms of performance and usability.
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In my experience the tools from larger vendors easily handle such amounts. I have no experience above 5,000 tables but up to that amount it should be possible. Some samples: Oracle Designer, ERwin. I myself use yEd plus an own case-tool. I find the essential feature that makes large volume manageable that a tool can auto-layout and auto-group tables that have strong relations between them.
For my interest: what problems are you running into? Can you add those to your question?