How to reduce dimensionality of audio data that comes in form of matrices and vectors?
Interesting ideas on finger printing, but that isnt going to work here, as you don't have a definitive sound you are working with.

To me, this seems a bit more like an image processing problem. So instead of thinking how you could reduce dimensionality, could could try and combine your data together into "images" that digitally represent the sounds you are looking at. Then using standard image processing techniques. I say this waving my hands around vaguely, as I don't know of specific ones, but have enough understanding of edge detection, feature detection and applying map/reduce type methodologies which might be able to give templates for what you are after.