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To be clear, the ignore patterns are only applied within the project directory tree, not to the path to the root, so as @techee said, unless the mount points are inside the tree they will not be filtered. Any filter applied to the path to root could only ignore the root and therefore the whole project, which does not make sense, the plugin would not do anything.
The point of the plugin is to scan the filesystem and optionally scan all files for symbols, so if the filesystem where the project is stored is slow the plugin will be slow. Possibly you can improve the SSHFS/NFS caching, but startup would probably still be slow as everything in the cache is validated.
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