If a huge number of tables has become a database performance bottleneck, I have to agree with Rimian. You can programmatically define your own content types and then develop your own content type model using the Node API.
API documentation and an example of how to do this: http://api.drupal.org/api/drupal/developer--examples--node_example--node_example.module/6
The code stream is basically:
- Make Drupal Recognize Your Content Type
- Define the fields that must be completed using the forms API
- Determine how each of the Node API functions should behave (view, load, save, etc.).
This allows you to control how things are stored, but it still gives you the opportunity (and all the modules provided) to use the hook system for calling Node APIs.
Obvious drawbacks are absent in all functions / modules that directly depend on CCK for their functionality. But with> 1k tables (which means a huge amount of content types and fields), it looks like you're already at that level of user experience.
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