"I do not know if they like soup."
Translation:Ik weet niet of ze van soep houden.
"Of ze van soep houden" is a subordinate clause, so the verb goes at the end.
Of is also used to join coordinating conjunctions, I'm assuming there is a difference in the context of it meaning "if" (whether) rather than "or" (an alternative) ?
So would it be correct to say "Ik weet niet of zij de soep lekker vinden"?
If you use "soep" instead of "de soep", then yes! There's no article in the English sentence, so it's about soup in general.