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I only recently started to poke multisite, as far as I understand you activate plugins per-site by activating theme in that site’s admin area. You can switch between backend of different sites in
Super Admin > Sites > (hover cursor on site) > Backend
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Server load is not about quantity of plugins, but quality and performance specific of plugins used, amount of page views and caching.
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You can try plugin like Clean Options to check for leftover settings, but it is still manual work to properly determine and safely remove options. Leftover database tables are even more of a mess.
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Inactive plugins are not processed in any way. WordPress stores information about active plugins in database and only loads those on the list. Rest are merely ignored files on hard drive when inactive.
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