How are you supposed to write villainous characters if they don’t do villainous things?
Of course villainous people do villainous things in narrative. Voldemort killed Harry’s parents to drive the narrative but that doesn’t negate that it’s murder.
The things Hook does are still villainous things that are getting turned into romantic moments and never brought to bear. You (and the show) are giving them a pass from ever having to face the consequences of those actions. Simply by saying “oh he was a villain then” doesn’t cut it. That doesn’t lessen his actions nor mean that he doesn’t have to pay for them in some regard.
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"He was a lot of things to me" "The only conclusion was love"