It sounds a good enough idea to me, you just need to be sure that the new battery(ies) are very well secured to prevent any possibility of movement when the boat is rolling, and keep in mind that you need to consider a worst case scenario such as a knockdown. The last thing you want then is for batteries to be getting thrown around.
In regard to cable routing, be guided so far as possible by the existing arrangement where possible. Any holes drilled through longitudinal or transverse frames in the hull structure should be located at the mid depth of that structure to minimise the stress at that point. They should be perfectly round so as not to provide any notches from which cracking can spread. Glassing in tubes for the cables to pass through sounds a good idea as this will help to replace any strength lost as a result of the holes you have to drill.
Also keep in mind how you propose to keep those extra batteries charged, is your present system up to the job, or can you improve things, say with a solar PV system. Having extra batteries serves little purpose if they are allowed to run flat.
Good luck and I hope it all works out well.
