Is it possible to have paths and barriers for the AI at different heights? So for example the ai would walk on a bridge in a straight line and then immediately above that in parallel is another bridge the ai can walk on, or perpendicular.

You can't have paths and barriers at different heights because they are of infinite height. If you place a barrier, for example, that barrier extends infinitely high and infinitely low. However, I'm pretty sure that if you put one bridge directly over another, you can (and unavoidably will) use the same hubs/connections for both, which is kind of a workaround.

I thought this might be the case.