1. Turning the Plugin System On or Off does not have any impact on the amout of queries.
2. Memory Footprint is not a such a big issue. In most cases, forumcache (which is loaded on every page) for example will be a lot bigger then the plugins.
Having to eval() the code all the time, that is an issue.
Therefore, complex plugin code (especially in high-traffic places like global.php, postbit, showthread, forumdisplay, etc.) should be moved out to include files.
(Could even be done automatically. I wrote a proof-of-concept hack that writes include-files if the plugin-code on one hook is > X bytes long.)
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