Disk Image Mounter does not show hidden files/folders when it opens an ISO file
Solution 1:
You have to:
- select ISO file in Caja;
- do right mouse click on it, select Open With → Disk Image Mounter (or mount it by Disk Image Mounter with double click if it is default application);
- press Ctrl+H to show hidden files (or View → Show Hidden Files).
About "why" part - it seems to be by design. Caja respects the user-selected Show Hidden Files option for folders.