It may be worth investigating an upgrade to OSSEC 2.9.0. 

According to the changelog, there's 2 potentially useful fixes that may 
help you out https://github.com/ossec/ossec-hids/releases

   - Avoids computing hashes multiple times to improve performance
   - Syscheck improvements

Alternatively, try bumping up the amount of allocated CPUs. Maybe you've 
finally topped out the server node? Do you have historical graphs of CPU 
usage during scan times?

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