It's impossible to use the remote in navigation mode in Space Exploration. Not sure if there's a work around?

Yes it is and i have no glue how to change this behavior, sorry.
personally i don't have really problems with this. I do research and use auto target, this is sufficient for most cases.

I'm aware auto target is functional, but there's no reason that the SE advertised orbital ion cannon mod should be unable to fire in nav mode. MIRV from klonan works, artillery works, but for some reason the remote in this mod is unusable.

but there's no reason < but there is one, a technical. It is not intentional that it does not work. ;-)

Orbital Ion Cannon (0.13-0.18) was developed by Supercheese long before Space Exploration (0.17-..) So the technical implementation does not work in the "navigation"- mode, which is only a hack using the good mode.
I just made it work again for version 1.0+ and adapted some aspects for Space Exploration, like support for multiple interfaces, hence "SE-Edition" in the name. To fix the problem hopefully, i would have to reprogram the complete implementation of how firing is done. This is already on the to-do list for other reasons, but right now there are more important things to do.
So currently you can be happy that you can use Orbital Ion Cannon at all, even if not perfectly in every conceivable situation. :-)