I certainly have no idea how large your boat is, what size and how heavy your batterys are, or much of anything else that would give me a very good way to answer you. So, has that ever made any difference to me?
I'd guess that any boat that has a pilothouse could easily handle the shift of 150 pounds or so of weight. Its likely that you could move the batterys without much problem with cable length, though you might have to move up in cable size. Once they are running it more likely that you will actually have shorter wireing runs to the real electrical use on your boat.
And a word on that. I see very few boats on which the owner's really neglect their engines. I know that sounds wrong, but most folks won't stand for an engine that doesnt' start easily - sort of the McDonald's mentality we've developed in a way. We got used to instant and by god its instant we want. So, if your engine starts reasonably well it sort of knocks holes in the notion that the real big job a battery does is start the engine(s). In fact the battery is dealing with the engine(s) for just a few seconds per trip, and the power that is removed starting the engine(s) is replaced within minutes at the most. No, the real deal for batterys is not the engine starting, its the constant use of everything else. You're out there on the boat with a VHF or two running, the depth finder pinging away, a chartplotter doing its thing, maybe Hendrix on the CD, the cell phone plugged in, someone blowing off the slime with the wash down pump, and a baitwell circulating to its heart's content and you're worred about the power draw of starting the engine? Sorry for ranting .....
Sure, move them, mount them as low as possible but where they won't be flooded in case you begin to take on water. Make sure the space is ventilated and make sure your cables are of sufficient size to handel the loads. Box 'em up and tie 'em down. Go catch big fish!
"For every complex question, there's a simple answer. And it's wrong."
(--H. L. Mencken)