"Node" refers to a piece of software known as a client. A client is an implementation of Ethereum that verifies all transactions in each block, keeping the network secure and the data accurate.
You can see a real-time view of the Ethereum network by looking at this map of nodes.
Many implementations of Ethereum clients exist in a variety of languages. What these client implementations have in common is they all follow a formal specification. This specification dictates how the Ethereum network and blockchain functions.
Data and contracts on the Ethereum network are encoded, but not encrypted. Everyone can audit the behavior of the contracts and the data sent to them. However, you are always free to encrypt data locally before broadcasting it to the network.