Join Date: Aug 2006
Location: Arlington, VA
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It's done all the time. Never heard of a significant problem, providing the basic installation is correct.
On my boat, I have one large house battery bank consisting of six Trojan T-105 batteries. Two of these are under the nav seat on the starboard side, four are located under the berth in the owners cabin on the port side. The two banks are connected thru a hefty 1-2-BOTH-OFF switch which is left in the BOTH position.
The cables connecting the two banks are about 12 feet long, and are of heavy guage (1/O I believe). They probably should be larger, though.
Never had a problem in many years; everything works as it should.
That said, it's definitely preferable to co-locate all your house batteries, rather than separating them. But, if that's not possible, I don't see why you can't separate them if you do the proper engineering.