In the "biz" these are called in-house or Indy programs. Some affiliates prefer them and sometimes in-house programs pay better. They can be a little riskier because you can't rely on the networks to pay you, but if you go with a known Indy that has a reputation for paying affiliates, you would probably be OK.
Preferred if they are using name brand or well known affiliate tracking software as some no name or low end programs don't track that well.
Many merchants that have good program offer dual options. They may be on CJ plus have an in-house option. There are some pros and cons both ways.
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