Thanks for your response. I understand that adding indexes will add some extra time to replicate all records. But an increase of >10000% ?

As you see in the log there are 4919 command/sec when writing without indexes and only 64 commands/sec with indexes on the Subscriber table. It's a huge difference and I really can't believe this has only to do with the indexes.

We had exactly the same replication set before on another server where the indexes added a few minutes to the replication time, but not a difference of almost 3 hours(!). So I really think the error has to be somewhere else:(