Then you need to maintain it all the year and hire the crew, and rent an area to 'park' your ship. Cheaper or not depends on your load, location and expected duration of campaigns.
The Spanish Oceanographic Institute own five ships and a ROV for example, with labs and all the stuff http://www.ieo.es/flota
For long expeditions (antartida) larger ships are shared directly with the army.
Yes, but in many places you can only do work in some months each year (because weather) and can only map the bottom if the ship is not reserved for studying other things (fisheries, ecosystems, geology, red tides, black tides, phyto blooms...). And people have children and family and teach duties. Your campaign just can't last for 12 months.
Having a ship in a port for eight months is also expensive and moving a big ship eats a lot of gaz, so for coastal areas... "We're gonna need a smaller boat".
