I assume you are talking about small boats, not ships. I am also assuming that you are looking for voids, delaminations, etc. in fiberglass, wood, or other similar materials, not in steel.
This has been and is being done through a variety of methods, I think. It will depend on the the choices made in the lists above... materials, type of problem sought. Front surface heating for transient IR can be used. Through heating for transient and steady state IR can be used.
While I have not done this specific examination, nor done the calculations for it, I would lean to using heat transfer analysis to predict what could be found under what regimes. Using FEA for heat transfer analysis is something I have been preaching for a few years. Samples of what I am talking about are on my website in the form of papers that I have presented and other examples.
You might also look to the NDT community for help. Either through NDT sites or through searches on NDT and IR. One probable hit would be Thermal Wave Imaging. A related area from which you could learn methods and approximate conditions would be aircraft inspection.
Let me know if I can be of assistance.
Jack M. Kleinfeld, P.E. Kleinfeld Technical Services, Inc.
Infrared Thermography, Finite Element Analysis, Process Engineering