We're a 'do what you like' household. But unless you're staying for hours and might like to put your feet up I'd recommend shoes on (especially if you aren't wearing socks - because I hate feet), we have a substantial mat for wiping.
We have wooden floors and rugs, and a dog and two cats (trust me they don't wipe their feet). When the dog was toilet training we encouraged guests to keep their shoes on, I stepped in shit in my socks more than once!
We also have a house where access to the back garden is through the house, so if we're having a BBQ you'd have to carry your shoes through and put them back on. I'm sure all this will change as soon as the expected-any-day DC starts licking the floor (though only briefly, once they've grown an immune system it'll be back to normal). I'd usually expect shoes off upstairs.
If I'm at someone else's house and it looks like they might prefer it (wall to wall carpet/shoe rack/no dogs/v. clean floors), or my shoes are dirty, then I'll take them off (I was raised in a no shoe household, my mum brings her slippers when she visits), if they traipse through their own house in their wellies with their dogs I'll leave mine on too.
I don't see how it's difficult to read shoe cues, if in doubt I'll start taking them off (I would generally assume shoes off unless I know better or their floors look a bit ming) very slowly and wait for the host to say otherwise if they'd rather I kept them on. I don't generally omit socks though, I would be less comfortable if I were barefoot I think.