Pretty sure for .apk files, since it's just the file that will install an app onto your phone, it will give you an update prompt when you download a new .apk and try to install a new app through it if the app name is the same as the old one.
tl;dr: No, you won't have to uninstall it, lol.
Though uninstalling the .apk file is fine since it's not the app itself.