I don't think I would want to give up precious inside storage space unless just absolutely necessary. We always don't have enough storage space as it is. The best spot for the batteries is OUTSIDE with proper venting for gases and drainage for boiled out fluids...
I have seen several good install of batteries using the TRUCK SIDE MOUNT TOOL BOX. The 48-inch sixe is great for up to four 6VDC GOLF CART type batteries. If you only go for two batteries which will give you around 225AHs you can always use the extra space in the side mount box for outside items storage. Your stolen two 12VDC batteries were probably around 200AHs or less.
This is what a 48-inch side mount tool box looks like. Available from AMAZON and any number of auto parts places...

Getting one with the enclosed latch is probably the safest to have. Just having one with a lock clasp would not offer much resistance for thief.
This is good install idea across the trailer tongue preferable up near the front of the trailer...

You would drill down through the tool box from the inside through the trailer tongue. Then use the ROUND HEAD STOVE BOLTS pushed through from the bottom where there would no place to cut the head of the stove bolt bolt off from the bottom. The bolts and washers would be on the inside of the box...
Inside would look something like this...
You may want to use a battery strap across each battery attached the sides of the box to keep the battery from bouncing up making the terminals touch to top lid when closed.
This forum guy user 'GILLDAWG79' cut his vent hole opposite each installed battery as shown here and used a sink drain bottom from LOWES for vent.

Sample photos from google images-Gilldawg79
The inside area opposite the batteries is great for installing BLUE SEA TYPE terminal block and fuse blocks as needed. The outside of the box is also great to install BLUE SEA 4-position OFF-BAT1-BOTH-BAT2 selector switches..
I always make everything with ANCOR TYPE 4AWG battery cables and ring terminals. All of the BLUE SEA ITEMS will have the lug mounts for nice looking battery connections everywhere...
Since your battery cables have been cut off you may have to add a BLUES SEA junction type BATTERY TERMINAL BLOCK just at the trailer frame and then run new wiring from there to the battery box...
While you are at it also note the PROPANE are also big targets for thieves... I mounted a long length pad log under the cover where the screw down lever is located. Of course being a standard lock this will be easy picking for the thieves but may slow them down.


The idea for me is to have outside lighting that comes on when someone walks up. This could also send you an alarm inside your house... My trailer has battery operated wireless motion detector modules on both sides of it from AMAZON that will turn on my trailer outside lights as well...

Certainly ashamed you have resort to things like this. A good dog would help out as well... Insurance is great also...
Roy Ken