Whether they use BDB or LevelDB is not relevant because those blk files are not BDB or LevelDB files, so indeed that does not make a difference.

That their headers have a different format does make a difference (and I would not be surprised if they started using merged mining at the time of when your patched Armory failed).

In order to support their slightly different block format, you'll need to modify the class BlockHeader. I would recommend, for the time being, not bother making a program that supports both bitcoin and namecoin without recompiling.