The 2nd is not natural.

Both are great, I agree, I would add a comma to separate the information: I visited a village, which has many beautiful small houses, yesterday. A village, which I visited yesterday, has many beautiful small houses.

I think both of them are right.

The first., though a couple of small changes are still needed. Because you are using 'many', it needs to follow with the plural form, 'houses', not 'house'. As well, 'yesterday' is in the wrong position and needs relocating. There are a couple of possibilities: "Yesterday, I visited a village which has many beautiful small houses" or "I visited a village yesterday which has many beautiful small houses"