I'm now near the end where I need to destroy the two shuttles. I need to hack the Rep, but it will cost me 3 nanites - I only have ruddy 2!!!

I don't have any early saves, am I buggered?

Update:

Now need 100 nanites for the actual resonator. Trying to mine naites from the hybrids, but only getting 5 per 10-20 hybrids! I think I'm gonna chuck in the Tri-Optimum towel!

You can go back to, say, the Med/Sci level and farm a few hybrids for nanites. They respawn. Hydroponics works too, since there are usually a few hybrids right outside the elevator.

If you still have a lot of surplus cyber modules, there's a psi power that lets you turn ammo/etc into Nanites. Tier 4, "Molecular Transmutation". Not really practical, the Recycler item is preferred, but if you can't afford the Resonator then you can't afford a Recycler either.

WTF, you should have hundreds of nanites socked away by that point in the game. What on earth have you been blowing them on?

Well if it's down to you quitting the game due to your very poor financial management skills, I suppose there's no harm in cheating yourself a few nanites. Google around, there's a simple console command to give yourself some.