USB ports usually have a power switch IC to protect them, for example
http://www.ti.com/lit/ds/symlink/tps2549.pdf
Indeed, without this, one could fry a computer's motherboard just by inserting a bad USB device, shorting the port with a metallic object, etc so it is in the interest of computer manufacturers to always include the protection IC so that they do not have to deal with returned computers with fried ports.
Y cables have been around for a long time because of external hard drives and DVD writers. From the post you suggested, I would say 1) and 2) are taken care of by the protection chip. Indeed there is a risk of 3) in principle which you can resolve by first connecting both grounds together, which usually is what happens first as you insert the USB plugs into the receptacles.