I believe the map limit for Cave Story is 128. Although if you can help it, I'd suggest replacing existing maps instead of adding new ones.
That's weird, the duplicate map feature in BL seems to work okay for me. Might be a problem with version 0.4.5.0, but obviously that can't be helped much in your case.
I'm not aware of any specific limit on the size of maps, but I do know that the game will let you make maps that are pretty darn big. Generally, one design practice we try to discourage is to make your maps too enormous. Even in the case of mods that did this gracefully, like Jenka's Nightmare and CS Redesign, it can make the mod hard to navigate. Also, not sure if this matters, but if your map exceeds certain dimensions (don't know the dimensions off the top of my head), then the map system won't work on that map.