Is there a way to export an object without all of it's inside geometry? For example: If I had a cube and hidden inside it's bounds there was another, smaller cube and I joined/merged/combined them into one object, is there any specific action I can do to make the resulting object just the outer cube without any unnecessary inside clutter e.g. the smaller cube?

Of course we're not talking about something as simple as two cubes here, it's a model of an AK-47 assault rifle and I used a lot of parts to make it and there is a lot of said clutter. Removing all unwanted clutter manually is not something I'd like to do or even attempt.

So is this something Blender can do or do I need to look to mods or another piece of software?

Thank you in advance for answering.
I want to say the answer is no - for what you're describing. 

Maybe there's a script out there that does it for you but it sounds like something you might have to write up yourself. ?

In my experience, I would typically hand-delete them, separate them.

It also sounds like a lot of work to fix and might need to look into another workflow method...

Good luck!