Hi Mario,
Ideally I cannot recommend you to delete entries directly from Dunning table FKKMAKO and FKKMAZE as these entries will have dependencies on other FI-CA functions like Collections, Write-offs, Account Balance etc.
As you have already mentioned that your performance traces shows FKKMAKO and FKKMAZE have impact on performance, I would recommend you to check for any standard SAP Notes/KBAs first.
Please have a look at the below KBA:
2006250 - FPVA performance problems due to SEPA mandat check
SAP Notes:
2269280 - Performance issue in FKK_READ_DUNNING_HISTORY
2234724 - FI-CA: Schlussrunde in FPY1/FPMA/FPVB für gesperrte GPARTs
2216402 - FPM3: read from archive
2225483 - Long runtime in function module ISU_DB_GET_POS_DISC_RELEVANT
Also please go through the SAP SCN Wiki's which explains few aspects of Dunning and related performance issues:
https://wiki.scn.sap.com/wiki/pages/viewpage.action?pageId=375621080
https://wiki.scn.sap.com/wiki/display/UIndustry/Dunning
Technically, try to introduce custom indexes to table if that helps.
After all these, if you really want to delete entries, then for each Contract Account get the current balance, check if its zero and also no related FI-CA Collection process are active and delete those entries, but this should be last option.
Hope this will help you in right direction.
Thanks,
Srini