Yep.
Best bet if you have the time and money is to regularly visit a chiropodist. They can properly cut off any likely-looking nails, keep them trim, and will tidy/file any loose skin or blisters.
I had all the things you mention... Loose toenails, thickened nails, and fungal infection. Loose toenails are best off gone and if it's possible they'll cut them down, otherwise you need to wait for nature to take its course. I don't think the raw skin underneath is that sensitive or painful to be honest, and it's only a week or two before it seems to get a tougher film, which I guess is the beginnings of a new nail. They'll use a file to thin down the thick nails, and your new tidy feet will make it easier to attack the fungus, but they'll likely advise you to apply Tea Tree Oil to the infected area.
I see the chiropodist every 8-10 weeks and it's £30 a pop. It does sometimes seem a waste of time as now that my feet/toes are in better shape, it only takes 15 minutes for him to trim them down and thin the nails, but I think it's worth it if you are running seriously.
Incidentally I apply surgical sprit to my feet at least 4 times a week, and still apply tea tree oil to the previously fungussed nails, prevention better than reaction. I now can get through endless hours of running without blisters, even on a hot day or if my feet get soaked 10 minutes in. Whether it's the effect of the surgical spirit, the natural toughening of my feet, or a combination of both, I'm not sure.
But to actually answer your specific question, my chiropodist commented that if you go running in the mountains you've got to expect some "wear and tear" to your feet and nails, and unless painful, then it's nothing to really worry about.