You probably play in a pakset-language comination which does not support an appropriate citylist.
The citylist is a txt.-file called "citylist_xx", where 'xx' is a language code. It is located in a folder named 'text', either directly in the simutrans folder (if it came with the game) or in the pakset folder (if it came with the pakset) - the one in the pakset-folder overwrites the one in the game folder.
Since you say "a lot" of the cities are named simcity, I suppose not all of them are. This indicates that a citylist for your language does exist, but is too short. If it is a pakset-citylist, just rename to something else so it won't be used anymore, it's possible the citylist in the game folder provides more names. If not, you can just add names in your citylist depending on your location, or you add them from another language.
However: The citylist is only used on generation, so it would fix a new map, not your current one. For the current one, you would have to click on each townhall and change the name directly, as the public.