The ferry to Orkney/ Shetland from Aberdeen has open decks. It may be worth considering other ferries to Orkney though, as they're shorter and probably have more flexible running times, which will allow you to connect with travel to North Ron more easily. If you get the ferry from Aberdeen, you'll probably need to overnight in Kirkwall. Both times I've been in the past two years, I've flown Aberdeen-Kirkwall, which is quick and convenient but a bit expensive.
The flights from Kirkwall to North Ron are quick and very cheap, particularly if you're staying overnight. They seem to have quite a low baggage allowance (15kg for everything) but aren't actually too strict on it in practice. The planes are very small. If the weather's good, you get lovely views over the archipelago.
Ferries can get cancelled because of bad weather but so can flights. This year, there were no flights in or out of North Ron for about two days because of bad weather when I was there. Then, the flight I was booked to leave on got cancelled because of 'technical issues' and I had to stay another night (not the worst thing to happen, to be fair).
Basically, there aren't simple answers but there are a variety of options. All of those options could come unstuck though!
I'd also add that North Ron is totally great, the Obs is really nice (and excellent value) and the staff are friendly. It's also a fantastic birding and wildlife experience.
