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OK, I made a little investigation.
It seems that serialization/de-serialisation in https://github.com/jenkinsci/jacoco-plugin/blob/master/src/main/java/hudson/plugins/jacoco/ExecutionFileLoader.java
takes a lot of cpu, also load doesn't not spread evenly on all cores (I used htop).
In our case I'm speaking about ovirt project (~3800 classes).
iftop doesn't shows significant network traffic and iostat also doesn't shows significant load.
So analyse of the same jacoco.exec file on idle jenkins taking 30-50 seconds, but on production jenkins it can take 30-50 minutes.