I agree with @koreader .
Postscript: Since MN 3.5 which has been released this week, built-in ABBYY engine could make PDF searchable. (now provided as a subscription)
To see the demo video:
According to our Users feedback, Spotlight and Alfred could be used to search MN notebooks and docs(https://cforum.marginnote.com/t/topic/2128). Mendeley works fine with MN.Maybe some workflow will suit you well. But it needs to explore.