There are many things that can slow down a JIRA installation. Add-ons are one of them, but it's usually a compound problem where the add-on itself is fine, but lets people set up configurations which cause issues.
The only way to "tune" the system to avoid slowness caused by add-ons is to not use them really.
You will need to go into a lot more detail about where the perceived slowness is, patterns of it (times of day, certain screens, specific fields on screens, how it affects some or all users, which project, is it the javascript or the back-end that's slow, and and and)
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