Ferry from Aberdeen to Orkney

At Kirkwall the ferry arrives at Hatston, two miles out of town. As well as taxis a bus, the X10, is waiting to take you into town.

Whether the Scrabster route makes more sense is in the eye of the beholder, you certainly see a lot more that way, and could deviate via John OGroats and Duncansby Head. The Scrabster route lands you at Stromness. I would book somewhere there in Stromness a very historic and interesting town, which gets rather overlooked by many guidebooks.

Also you have the Pentland ferries route from Gills Bay to St Margarets Hope on Orkney, then over the Churchill Barriers to Kirkwall.

The fun and different route, just reopened, which I really want to do, is to fly from Aberdeen to Wick, thence to either ferryport for Orkney.
From Wick Airport to either ferryport is easy by bus, or there is local car hire in Wick.
There is no good reason why you couldn't do the morning train from Aberdeen to Thurso (change Inverness), foot passenger on the Scrabster ferry, then the same connecting X10 bus to Kirkwall.

Don't overlook flying from Aberdeen to Kirkwall. There are several daily flights and prices are reasonable due to the oil industry traffic. Taking a rental car on any of the ferries is comparable to airfare. In Kirkwall, you can get a car at the airport or the next morning in town, depending on your flight time. My wife isn't very keen on a six hour boat trip in the often rough seas. Returning, I don't think Gills Bay or Thurso will have a one-way car rental. You'll have to ferry (or fly) to Aberdeen to get a car for your next chapter, unless you plan on public transit. Renting a car in Aberdeen and making the trip to Thurso or Gills Bay part of the adventure, and taking the car on the ferry there and back might make $$ sense depending on the number of people traveling. Cars are a little more expensive in Orkney.

Loganair has flights between Aberdeen and Kirkwall. I fly Loganair quite often including three times in December.

If you want a taxi at Kirkwall airport, arrange for one ahead of time. They don't hang out at the airport. I found this out the hard way.

I agree with Frank about the taxi situation at the Kirkwall Airport. I've used Craigies 3 times and recommend them. All 3 drivers have been so personable and interesting. They all had me laughing!

https://www.craigiestaxis.co.uk

I'm a terrible sailor so I've flown the times I've gone to Orkney. If you do decide to go with the ferry, and do FB I suggest you follow the Northlink Ferry page. They try to give a heads up if they think there will be service disruption due to weather.

https://www.facebook.com/NorthLinkFerries

Also from Kirkwall airport there is a bus into town, every 30 minutes all day, plus the odd extra on routes other than the dedicated shuttle.