I've lost one 12V battery over the years to thieves that hit the storage lot. They drove in, cut battery cables, threw the batteries in a truck and were out in short time. I used bike cables after that, but were never a great solution. Locking boxes were too expensive, so I found this solution that had quite a few positive reviews:

The website is: http://www.b-drvbatterylock.com/

They make a 12V or 6V standard battery box lock and the 6V can be purchased in pairs which is what I have above. I supplied the keyed-alike locks for an addl $16, but this should make the bad guys move on.