There was a really extensive discussion about filtering bots in the PHP tracker on the German forum:
To sum it up:
There is no rule that fits every use case.
Piwik by default ignores bots it recognizes via user agent. (But you can disable it)
You’ll probably want to build your own bot detection on top of device-detector
Maybe track users you detect as bot to an separate site-id or add a Custom Dimension/Variable, so you can create segmentation to differentiate between them.