I would like to know what is the accepted business practice in the USA, if to calculate commission on the FOB price or on the CIF price? In other words, when commission amounts are calculated, are they computed deducting shipping costs first?

It will depend on the industry,

Often the commission for salespeople are based on the actual sale price including all overhead.

It's the freight forwarding industry, which is what I work in, I can tell you that the forwarder on either end split the profit on all shipments they do so for FOB, FCA and all shipping terms there is always a commission added.

I would need more info though, are you the shipper, receiver, forwarder? If you're the receiver there shouldn't be a commission charge in most cases.