Very interesting stuff, we've done a lot of underwater scanning sonar but not laser yet. Is there any issue with water clarity? I would imagine that reasonable visibility is required. Also, do you use scanning sonar to provide the overall location of items, as per the last image?
We locate our scans typically the same as a terrestrial job - a choice between or combination of black and white checkerboard targets, sphere targets and cloud-to-cloud registration. To geo locate scans, or to locate them over slightly longer distances then yes solutions such as sonar LBL (like in the last image) would be used.
Yes water clarity has to be considered. However unless it's like gravy, typically subsea laser scanning works fine and clarity is not a limiting issue. We use different models of equipment for different conditions (including water depth, clarity, deployment method, total area to be scanned). Just like terrestrial laser scanning with regard to equipment choice its 'horses for courses', and again like any other surveying, having the right equipment is only 25% of the battle, you need to have experience and understand what you should and should not do!