I agree lipos are incredibly cheap these days.
You read some accounts of lipos out there, and you'd be forgiven for thinking you were installing a nuclear bomb in your boat!
I agree with the main points being made about using a balancing charger and over discharging. It should also be understood that lipos contain an internal fuse that disconnects the cell should it go under voltage. This is a safety feature built in so if you run them down to far, the pack is just kaput, it shouldn't go up in smoke.
For submarines, you might want to take a look at LiFE/A123 batteries. These are lithium based but a different chemistry, and as such they have a few advantages over lipo's, far less sensitive to over discharge, tough cylindrical casing and very long cycle life.
The trade off is an initial higher upfront cost, a restricted range of suitable chargers, and a slightly lower energy density. The cell voltage is also different on these batteries, 3.2 versus 3.7. Depending on the application that can work for or against you.
Life batteries can be purchased via ebay, Hobbyking etc. Unfortunately not many people selling them here in the UK at the moment.