As of this week, RetroArch supports multiple mice in all cores that have their own support for one or more mice. As long as the original emulator that the libretro core is based on has mouse support, the libretro version should as well.
If a core which should have mouse support doesn't work when thus configured, there is at least one libretro dev who is actively looking for cores to fix for mouse support, so new github issues are welcome.
In other words: what are you trying to do that isn't working?