Yeah, I tend to add in my EMBs after the fact, by hand. It's a huge chore, especially for games like Mystic Ark or Gun Hazard which, as mentioned, have thousands of the things. (GH's total was around 3000, Mystic Ark's around 6000.)
I also tend use embedded pointers to create easily-movable pointer tables. I know that's not what they're originally meant to do, but it's a quick-and-dirty hack that makes a lot of sense for games that have a lot of small blocks stacked one after the other. Basically, I figure out how the game gets the address of the pointer table - whether it's through another 24bit table or some LDAs or whatever - and rig up a write to that address. Then I set up an embedded pointer for each pointer in the table, and map it to the corresponding string later in the block.