Looked into this a while back. WhatsApp MCP servers attach as a second device to WhatsApp and pull down your message history.

Most of the ones I've seen on github do not store the messages encrypted locally.

When evaluating these tools, check to see what they store unencrypted on disk. A quick search shows that only one seems to check the boxes:

https://github.com/adelaidasofia/whatsapp-mcp

However I haven't tested it. And it does phone home, you may want to disable that before running it.