Speaking as a resident, the local usage is that Baltimore means Baltimore city. If you want to refer to the County, you say Baltimore County. I live in Baltimore County, but we border on Baltimore. Functionally, County is part of the name, i.e. Baltimorecounty, Howardcounty, Carrollcounty, PrinceGeorgescounty, etc. The options given when you go to enter a place name in WikiTree leave the word County out. We generally know what is meant (except in the case of Baltimore), but we smile patronizingly, knowing that this is all being done by outsiders. who, while not really ignorant, don't know their way around that well either!
Since there are excess categories at the moment, I would suggest keeping Category: Baltimore, meaning the city (which is indeed independent of the county, the only place in Maryland that is) and keeping Category: Baltimore County, which is how everyone refers to it. And get rid of Category: Baltimore City, since nobody says that.