According to the manual and the sticky label on the back of the passenger footwell fuse panel, slots F5, F12, F15, F16, F18 and F24 should be free. But when I looked F5 is occupied with a 10amp fuse, F15 - 10amp, F18 - 5amp, F24 - 15

There are no obvious modifications, is the manual correct or does anyone know what they might be?

(2007 HSE) 
Hung like Einstein, smart as a horse.

Both are correct really, they are unused but occupied. It makes sense to occupy the whole box at manufacture rather than leave one out here and leave another out there for different markets, for instance the F24 would be for the fuel burner market.

Also I would imagine the loom for these circuits would be in place and the fuses would serve to protect the loom from damage.

Ta EY,
So they can be viewed as spares then. 
Hung like Einstein, smart as a horse.

Yes, they can be viewed as spares.
If there is a wire on the outfeed end then it will serve nothing but a dead end in a socket somewhere, for ease just 'piggy back' it if you want to use it.

Note that even if a fuse isn't 'spare' you can still piggy-back on it given the right connector. I have some (sourced some time ago from eBay) which take two fuses - one fuse (normally the original one) feeds and preserves the original circuit, whilst the other (which can, of course, be of a different value) serves the piggy-back circuit.

I just got some piggy backing fuse holders, this is when I noticed that the I didn't have as many free slots as I should have.

Cheers.  
Hung like Einstein, smart as a horse.