I think that DLCs & themes only get deleted if you have a NNID setup in your emunand. If your emunand doesn't have a NNID, going into eshop won't delete the DLCs and themes.
I tested this with two 3DSs, both using GW, emunand 9.5, sysnand 4.2. The only difference between the two is one has NNID in emunand, the other doesn't. The one without an NNID doesn't get its DLC and themes deleted. The DLC I tested with is mii force. I also noticed that when mii force gets deleted on the 3ds with NNID, after I reinstall mii force, the save is still there. I don't know if this works for all DLCs though.