Slitherine

It appears that you can only off-load units from transports into an empty, non-neutral hex. If so, how can you invade Malta?

...The same way it was proposed historically. You must eliminate any unit there by air and naval bombardment before you can unload your invasion force. Very hard to accomplish, which was probably why an invasion there was never attempted during the war.

Does anyone know if it is possible to mod the game to allow you to invade into an occupied hex by attacking the unit that occupies it?

No, it's not possible.

That's a shame. Do you know why the game was designed like this, it seems a bit unrealistic. Surely invasions against a defended area are a high-risk and exciting factor in WW2?

There have been quite a few dicussions about this and we know it is something people would have liked but there were some technical issues which made it either impossible or too difficult to add at the time. Johan knows more of the details.