You should be able to decompile the maps using bspsrc or some similar tool. You can load the resulting .vmf into Hammer. No guarantees on being able to recompile the result successfully, though; I've never tried it myself, and it sounds like a pain in the butt honestly.
I know from experience that you CAN add or remove entities using a hex editor. Since the entity data is stored as a massive string inside the compiled .bsp, you can make any changes you need to inside that string PROVIDED THE ENTITY STRING IS THE SAME SIZE BEFORE AND AFTER! So if you add X characters to the entity section, you also need to remove X characters. It's pretty brittle and error-prone as an editing method, and this only lets you edit entities (not brushes or terrain, etc), so you may have a better time going the decompile-recompile route.
