If the mods use the template/override system, their files will not be touched by the upgrade. Some of these mods have to modify core files, so you will have to compare the list of mods' files with the changelog and see if any of them have been changed in the core version since the latest mod version. If so, you will have to merge the mod and core changes. If not, you can just re-upload the mod files over the upgraded Zen Cart version.