"Perhaps the master can loop through all of the children boards and send a serial command, if the child has found a tag it can respond and send it back other wise return false and the master can carry on through the loop."
Exactly, and described very nicely!
If you use RS485, then you can connect them all to the Rx/Tx pins, the RS485 provides the electrical separation between all the devices serial ports.
See Figure 5 in this Maxim application note.
http://www.maximintegrated.com/app-notes/index.mvp/id/723