It's good to check first.
This is the only officially recognised ticket office by the NP for Alcatraz trips that does not have agent fees or the need to buy other tours you might not want. Alcatraz is busy year round and it's worth pre-booking imo to save standing in queues with a possibility of the next boat filling up and having to wait for another.
It's usual for a hotel to want ID and your credit card details for security purposes and to charge the card with any extras you may have, food, drinks bill, telephone usage etc. You have to use your judgement but I wouldn't be comfortable using a private hotel that has a reputation for identify theft, or even a chain for that matter. It's hard to comment as this could be a rumour, or has it been proven ? What type of hotel is it ? Most bookings you can cancel and get a full refund, but I would recommend you check the reviews prior to booking anywhere else !!