Rental company asking for passport number etc.

A passport number only has name and number and therefore far less value than a driver's license or even a credit card. It is not that big a deal. I would not worry about it. If this is paranoid causing, you are in for a rough trip. This is low on the list of things to worry about.

You enter it when you check-in or book a flight online.

totally standard; many require a copy. They will have to register your passport with the police in most countries, not sure about the Netherlands on that, but it is standard. Would you rent your place to a foreigner without good ID?

Did you give them your credit card number when you booked? Now that is a piece of personal information I'd be more concerned about. Passport number is of no value to anyone on the dark web.

Your passport is your ID. Giving out the number and expiry date is normal. It is of no value to criminals (unlike your credit card number).

• It is a legal requirement in The Schengen Area for hotels to record passport details of all foreign guests.
• It is a legal requirement for air flights to many countries (US, Schengen Area, UK etc.) for the airlines to hand over passport details of all passengers before takeoff. You will have to give your passport details (usually on the airline's website) before they will give you a boarding card.

Just got back from our vacation in venice paris and amsterdam. Was asked for passports ot driver's license at all three. No t big deal. I'm wondering how was your place you rented in amsterdam with cityden?
Thanks