Are there any theories to explain its retrograde rotation?
Surprisingly, Earth also seems to play a part in the tidal effects on Venus: Whenever the two planets are at closest approach, Venus is always showing the same face to us.
How can they tell? All we see is clouds. (I believe you, really asking)
There have been some orbiters of Venus.
For example, the Pioneer Venus Orbiter had cloud-penetrating radar:
It orbited Venus for 14 years.