Say for example I like the look of an abandoned shack or a random house I come across, can I leave my valuables in a footlocker/safe/wardrobe without the fear of it going missing?

It's safest to test it by placing and item you won't miss in it go ing away waiting longer than 72 hours and then returning if its still there its safe, most places are safe to use as a home very few of them have respawning containers.