Hello Sailor Steve,
in my understanding "Handelsschiff" (Plural: "Handelsschiffe") is a more general term. "Frachtschiff" (Plural: "Frachtschiffe") or short "Frachter" is more specific and describes ships which transport cargo or freight. Actually a Tanker can also be a "Handelsschiff" if the Tanker is part of the merchant fleet ("Handelsflotte"), at least according to wikipedia.
Therefore I would say "Frachter" would be more correct, but "Handelsschiff" is understandable enough.
Hope I haven't confused you too much!
Mr. Fleck
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