Not necessarily a good idea unless you can get four in there, as you have no redundancy. If you have only 2 - 6V batteries and one fails, you have no power. With 2 - 12V batteries, you can accommodate a failure of one battery.
Larry
This is why most boats have a reserve/start bank as well as a house bank. I would agree if they are the only batteries on the boat though that two 12V make more sense..
In all my years working on boats I have seen perhaps one person correctly diagnose a bad battery out of a bank while out at sea or off cruising and remove it from the mix. With newer technologies like GEL and AGM this is made even more difficult without the ability to do an SG test as the OCV often looks fine, even when you have a bad battery.
6V batteries are also far more robustly built and will take a lot more abuse than their 12V counterparts will so it has been a very, very rare occurrence that I have seen a bad cell or bad battery out of a combined 6V bank than I have with 12V batteries.
Had a set of AGM batts just last week and OCV was fine but the bank was not holding a charge. One battery was okay to marginal and the other was near toast but still put up 12.6-12.7 volts, same as the other one. A 500A carbon pile load test backed up by a test with a $750.00 analyzer confirmed which was the really bad battery and which was the marginally bad battery. The windlass could have confirmed this had the owner known how to test it and what to look for.
I personally have no worries at all with 6V banks that only have two batteries so long as the system was designed correctly from the start and that would include a reserve battery.