Are they comfortable with ankle socks?

I would recommend a tall sock. I tried them with ankle socks and they didn’t keep the debris out as well and the rubbed pretty bad around the top where they are tight. Tall socks makes for a better gasket and keep the blisters off the back of your ankles.

does it fit any shoes?

Doesn't exactly fit my New Balance, rubber strap doesn't go forward enough to completely fit in notch on underside of shoe. Doesn't affect my use, but I'm not trail running. Might impact trail running on downhills.

Would these add any protection against snake bites...like would they be better than nothing?

Very little if any. You want snake gaitors for added protection against snake bites. Plus the fact that these cover suck a tiny portion of your lower leg means that even if they were snake bite proof, a bite just above the top of this gaitor would be unimpeded.

I have the salmon quest 4d boots in a size mens 11, will these fit over the tops of the boots to help keep rocks out while hiking?

I wear them over my 5 ten hell cats to keep my ankles covered with my riding pants. They cover the ankle sock gap well. They fit that need for me. I would guess that they would cover a higher hiking boot. But not by a lot. If you are not sure. You could order them on the Amazon wardrobe like I did. If they don’t work send them back. It’s a great option on gear that you aren’t sure about. Order the ones you like, pick the best one that works for you and return the rest. It’s a cool option.