I'm currently learning about AFDX networks and one of the main questions I have is the ability to do a mapping and port scanning of them. My understanding is that it is based on UDP connection using vitual links. Would simple tools like nmap and udp_scan work on this type of network?
You need to think about the network layers. Ethernet is a layer-1/2 protocol. IP is at layer-3, and ethernet doesn't care if it carries IPv4, IPX, IPv6, or any other layer-3 protocol. TCP, UDP, etc. are layer-4 protocols, which are on top of a layer-3 protocol.
AFDX is based on IEEE 802.3 (ethernet) at layers 1 and 2, and it should not know anything about what happens in the higher layers. Having said that, the devices connected to the network are very likely to have protections built into them. These protections may prevent such scanning, but that has nothing to do with the protocol itself. For instance, the switches often used will be designed to allow a device to connect to a predefined set of devices.