Just so we're clear, did you mean diseases (like from jungle and flood plains) or plagues (like the black death in the Middle Ages mod)?
I'd be interested to try some experiments with this...
EDIT:
So, I tried giving all Coast, Ocean and Sea squares 100 strength disease, and placed 5 boats in each type, then (for control) I placed 5 warriors in 100 strength diseased forests (I used forests so that i was still "changing" the disease property of the square).
RESULT: I couldn't get ANY unit to die from disease in ANY of my squares. I increased the treasury so they weren't disbanded and also tried both Chieftain and Sid difficulty levels, with no effect (except on Sid Carthage came in and whooped me pretty quick).
So what am I doing wrong?