My biggest concern with both is getting enough food and supplies for people to eat and drink, let alone conduct scientific research. The agricultural space needed to sustain human life would likely be larger than the top deck of the ship, even one of cruise ship size. You can grow food underground/belowdeck with Grow-lights, but I don’t know that you could get that Anartic bunker deep enough underground to stop the plants from freezing.
And then there is the problem of water. Desalination of ocean water can happen, but you would need a huge desalination rig. The bunker would probably need energy to melt ice.
Most boats have either an engine or a reactor that produces electricity, but that would need fuel. You may be able to use a water wheel if the boat is moving forward under sail, but using a sail limits the size of the boat.
It would be best to have both the bunker and the ship, because in the former you could drill for oil for the latter - but then you’d have to contend with the freezing cold to to do that.
So hiding this and keeping it a secret could be tricky, since the boat might need deliveries of supplies if it stays in international waters. Also a random Iranian ship might spot it someday and decide to investigate. This might not end well. So it might pay to have treaties with other nations to allow the boat to restock itself without causing a war.
Just some things to consider.