While playing or fishing in water, i've always worn shoes. While crossing water, I have not worn shoes. Cold, warm, shallow, deep, fast or slow has not stopped me from going barefoot. If it is an obviously high use area, I will find somewhere to cross for fear of hooks, glass, and such.
I understand the risks. I figure we run the risk of microbes and worms at nearly every point while backpacking. We sleep, eat, cook, wash with, and drink with nasty things.
Many would argue, for the sake of going light, that we take many risks to achieve our goals. Why skimp here? At best Ive used socks and old insoles. Amphib shoes seem to allow all the nasty critters in too!