I’m using Piwik on a Windows server running wamp and .htaccess, I read in another post that this can cause Piwik to run slow, but the person didn’t post how to fix the issue. Also, this website is just for intranet use only. It get’s maybe 20 visitors a day.
I’ve read somewhere that the Core plugin Device Detection can sometimes be slow. Try to deactivate it just to see if it helps.
I also spotted this: Tracking servers CPU saturation after upgrade from 2.1.0 to 2.2.0 · Issue #5019 · matomo-org/matomo · GitHub but it’s not in current Piwik yet.
Make sure you have enabled PHP Cache like APC. See: Optimize and Scale Piwik - Analytics Platform - Matomo